List of inconsistencies in the Halo series

"Science Team Leader"

- ONI Commander

This list is compiled to show the various discrepancies spotted in the Halo universe. This list is divided into two types of inconsistencies: conflicts and discrepancies. Conflicts happen when two sources disagree about a situation, subject or object. Discrepancies occur when a contradiction occurs within a single source. It is often difficult to decide which resource is "superior" to another, so conflicts are mostly listed in a chronological order. Likewise, it can rarely be conclusively determined whether a conflict is the result of an oversight on part of the author or editor(s) or an intentional retcon, unless this is specifically confirmed by the developers of the Halo franchise; such cases are noted accordingly. Additionally, there have been a number of cases in which an apparent inconsistency arises within an individual piece of media, only to receive a canonical workaround in a separate document; Halo: Reach and the Data Drops are an example of this. Many inconsistencies on this page are provided possible explanations, although it should be noted that these are only unofficial theories unless otherwise stated, and may not reflect the franchise developers' stance on the matters in question. For more information, see here.

If you think you can explain an inconsistency, do so here, on this article's talk page.

Halo: The Fall of Reach

 * The Eridanus II space dock is erroneously stated to be located in the Epsilon Eridani system in the chapter heading for Chapter 10. Throughout the rest of the book, Eridanus II is correctly referenced as being located in the similarly named, yet distinct, Eridanus system.


 * When Dr. Halsey and the Spartans are on a Pelican leaving the Damascus Testing Facility, Halsey tries to adjust her glasses but can't due to her space helmet. Despite this, after hearing John-117's plan to board the Covenant ship, she is said to tap her lip in thought.

Halo: Combat Evolved

 * The main view screen on the labels the as-of-yet unidentified ring as "Halo". The name of the ring is not discovered until the level The Truth and Reconciliation.
 * Cortana says she cannot begin to calculate the pulse range of Halo just after 343 Guilty Spark finishes telling her it has a radius of exactly 25,000 light years.
 * This can be accounted for by Cortana's inherent distrust of Guilty Spark's motives. Additionally, since Cortana is an AI with an insatiable urge to know everything she can, she may have tried to calculate the range herself regardless of whatever 343 Guilty Spark had told her.
 * Almost every Pelican dropship bears the marking "E419", on its side, despite the fact that each Pelican has a different serial number.
 * There is no canon explanation. This is due to only two Pelican textures, V933 and E419, being used to represent every Pelican in the game.
 * During the Warthog Run portion of The Maw, the player has to travel a direct distance of over three kilometers atop the Pillar of Autumn to reach the Longsword fighter, but the Autumn is only 1.17 kilometers long. The Longsword's launch bay is also at the end of the Warthog run. The front or rear of a ship is an unlikely place to store a launch bay, which implies that the Master Chief traveled from side to side, further straining the realism of the sequence.
 * During the level Assault on the Control Room, Staff Sergeant Johnson can be seen with the Master Chief at the time he was really with Captain Keyes searching for the Covenant's "weapon cache"; even though the Captain has been out of reach since The Silent Cartographer.
 * This is a result of Bungie reusing Johnson's model instead of creating another sergeant model. The same can be said for Gunnery Sergeant Stacker, who was treated as a generic NPC until Halo 4, when he was finally explicitly identified in gameplay.
 * In 343 Guilty Spark a body collapses on him on the Master Chief in the room where the Flood is introduced. It is unclear as to why this Marine was not infected when the Flood overran the personnel in the room.
 * This was likely done simply to add tension and suspense to the level, though it does seem rather unlikely from an in-universe perspective.

Halo: The Flood
The book states, "Consistent with his status as a veteran, the first alien to come around the corner wore red-trimmed armor, a methane rig, and a Marine's web pistol belt. The alien wore the captured gear Pancho Villa-style and dragged it across the deck. Two of his comrades brought up the rear." That is three Grunts in the Master Chief's sight. The next paragraph says, "Confident that there were more of the vaguely simian aliens on the way, the Master Chief paused long enough to let more of them appear, then opened fire. The recoil compensators in his armor dampened the effect, but he could still feel the handgun kick against his palm. All three of the Grunts went down from head shots." It is as if the extra Grunts that appeared simply disappeared. Only three Grunts were killed, which are the three original Grunts that first appeared: the leader and the two followers. But "...the Master Chief paused long enough to let more of them appear, then opened fire... All three of the Grunts went down from head shots." It is possible, though, that the Master Chief had simply expected more Grunts to appear; he may have simply waited in case more Grunts appeared, and then opened fire when he was sure there were not any. It is also possible that Master Chief was simply waiting for more of the three Grunts to appear, giving him larger target silhouettes to hit and reducing the possiblity of being surprised by a second group of enemies re-enforcing the first one.

Halo: First Strike
In Chapter 33, it is said that Will and Linda went out to secure the area. It then says that the Master Chief climbed up to where Fred and Linda perched. Immediately after it says that Fred and Grace disembarked the dropship implying that Fred was still in the dropship and it is presumed that it was meant to say Will and Linda.

Halo 2

 * The Halo 2 game case depicts the Master Chief fighting alongside ODSTs on Earth. In the game, ODSTs are not present until the level "Delta Halo."
 * In the cutscene Another Day at the Beach, the UNSC forces that land near Hotel Zanzibar wear ODST armor, reflecting the analogous scene from the Halo 2 E3 demo. When the Marines are encountered at the hotel during the level Outskirts, they wear standard Marine BDUs. Also, the location of the crashed Pelican does not match its position in game.
 * This is because Another Day at the Beach was cut from the game before release. The Marines from the crashed Pelican were likely switched to regular Marines later in the level's development.
 * In the level Delta Halo, seven dead ODSTs are strewn about quite far from the landing zone. However, In Amber Clad dropped only eleven SOEIVs in the opening cinematic. The Master Chief, the three ODSTs who land near him, the three killed near the intended landing zone, and the seven ODSTs means that fourteen SOEIVs should have been deployed. This is probably a deliberate reference to the number seven: 14=7x2.

Halo: Ghosts of Onyx
Kurt's rank was apparently lieutenant commander in 2545, as said in the prologue. However, he was still referred to as a lieutenant by 2551 later in the story.

Halo 3

 * Every Longsword fighter bears the marking 7-89 on its side, despite each Longsword canonically having a different serial number. This is the result of reusing the same model for all Longswords in the game.
 * In the ending cutscene of the level The Storm, all three UNSC frigates have the same serial number and all are labeled "Forward Unto Dawn"; one of the others is the Aegis Fate. This is also obviously the result of reusing the same model.
 * In the ending cutscene of the level Halo, the Arbiter is shown sitting at the bridge's helm after leaving the hangar. After the Dawn is cut in half by the portal, the Arbiter arrives on Earth in the front half of the ship, yet the bridge remains attached to the back half of the ship. Presumably the Arbiter moved toward the fore end just before the ship was bisected. However, the cutscene appears to occur in real time; thus, he would have had mere seconds to descend roughly two decks from the bridge to the main hull, after which he would have to move forward at least fifty meters to avoid being caught in the aft section.

Halo: The Cole Protocol
When Lieutenant Keyes is warned of the incoming Covenant fleet and asks what UNSC ships are nearby, the book first states that three destroyers are picketing, but immediately counters that the and three frigates would be unable to repel a Covenant assault. However, they are later confirmed to be destroyers, one of which is the.

Halo Wars
In the level Dome of Light, after requesting the first Rhino to be deployed, the radio operator on the will identify the player as "Harvest Surface Command" even though the level takes place on Arcadia.
 * This could be that the Spirit of Fire was still assigned to Harvest.

Halo: Reach
During the level Long Night of Solace, Colonel Holland once refers to the Covenant corvette Ardent Prayer as a cruiser.

Halo: Fall of Reach

 * When the Spartans are issued their MJOLNIR Mark IV armor, the armor is free of any insignia. After suiting up, the armor now has the Spartans' tags on the chest.
 * When Halsey puts on John's helmet for him, the helmet in her hands resembles the Mark VI's, with its raised brow, oval visor groove, and square mouth guard. In the next page as John wears the helmet, it is now the default Mark IV's, with its lowered brow, sleeker shape, and large breathing ports.
 * The bonus layout artwork for Covenant shows the Spartans wearing The Package Mark VI-looking armor in the initial sketches, then being corrected to Halo Wars Mark IV armor before the inking and coloring. It may be that the Mark VI in Halsey's hands is likewise an error that was missed in the correcting.
 * During the skirmish between the Unrelenting and the, Captain Wallace orders for a Shiva nuke to be fired at the Covenant ship and for their MAC to be fired. Just as the nuke is launched, a bridge officer confirms the Commonwealth MAC has charged to 100%. The nuke impacts the Unrelenting, dropping its shield and causing some damage near the bow, but the MAC is never seen being fired or impacting.
 * When Blue Team struggles with opening the door leading inside the Unrelenting, they appear to still be in vacuum. However, a Jackal without any breathing gear fights them after the door opens.
 * In the book, the first door to the inside of Unrelenting opened automatically, then shut to restore the atmosphere, with the second one having to be manually opened. The comic appears to have skipped the previous door and a comment from Kelly about the size of the door implies it's the first one they encountered.
 * During the raid of the, the captain tells her men to brace themselves before firing their guns in zero-g, as the equal and opposite reaction will push them backwards. The cover for Issue 2 of Covenant shows John standing on the outside of the Unrelenting firing in, and not having any trouble with his gun's recoil in zero-g.
 * The MJOLNIR Mark V was shown to have magnetic soles in Halo: First Strike, so it is possible the Mark IV also had them and John was utilizing those.
 * When the Spartans are briefed about Operation: RED FLAG, Halsey reports ONI has just discovered a new Covenant species, the Prophets, and shows an image of the Prophet of Truth. Yet in an earlier issue, taking place in 2525, the Spartans, Halsey, and Vice Admiral Stanforth watch a broadcast from the Prophet of Regret himself, who displays his image quite visibly.

Halo 4
John-117's size varies from cutscene to cutscene. John is five inches taller than Sarah Palmer; they are 7' 2" and 6' 9", respectively. However, in the level Infinity he is only minutely taller than her while in the Epilogue he towers over her by about two feet. In the middle cutscene from Infinity, she even jokingly tells the Master Chief, "I thought you'd be taller."

Halo: Silentium

 * It is established that Path Kethona is the Forerunners' name for the Large Magellanic Cloud, which is correctly stated to be 160,000 lightyears from the Milky Way. Later, when Audacity completes its second jump toward Path Kethona, the middle distance from the Orion complex is stated to be 87 million lightyears, or 60 million lightyears from the galactic border.
 * The reference to millions of lightyears instead of thousands is likely a typographical error.


 * The journey of 160,000 lightyears to Path Kethona is described as being an unprecedented and exceedingly challenging undertaking to the Forerunners, in particular due to the reconciliation debt involved with the long distance; even with a state-of-the-art ship specifically designed for the voyage, the trip is noted as potentially accumulating catastrophic causal strain. Strangely, no such difficulties are mentioned in reference to the trips to Installation 00 or its older counterpart, the greater Ark, particularly where the construction of the two extragalactic installations is concerned. Installation 00, at 262,144, lightyears from the galactic center, is roughly 100,000 lightyears more distant than Path Kethona; In Silentium, upon arrival at the greater Ark, it is mentioned that the lesser Ark is "hidden a third of the way around the outer boundaries of the galaxy". This would suggest that the greater Ark is situated well over 700,000 lightyears away, placing the apparent difficulty of reaching Path Kethona in a rather absurd light. While the comparative ease of voyages following the collapse of the ecumene at the end of Halo: Silentium and in Halo 3 can be justified by the galaxy-wide cessation of Forerunner slipspace travel, the construction and subsequent consistent traffic between the galaxy and the Arks for over a thousand years is more difficult to explain. When constructing the Arks, the Builders would have moved resources amounting to untold times the mass of Audacity over a far greater distance, yet the Arks' construction—which had already occurred at the time—goes unmentioned as an incident comparable to the Path Kethona expedition when it in fact far exceeds the Audacity's voyage as a technological feat.

Conflicts
For the sake of convenience, most conflicts are listed under the piece of media which introduced the conflict. For the purposes of this list, the established hierarchy of canon is mostly ignored; however, in instances in which two or more works have been developed concurrently and released within a short span of time of one another (e.g. games and their marketing material), the "primary" work takes precedence even if released marginally later than the "secondary" one. For example, conflicting information in Halo: The Fall of Reach is said to contradict Halo: Combat Evolved, even though the novel was released slightly earlier than the game. Conflicts which are persistent throughout multiple sources are listed in the "Several sources" section.

Halo: The Fall of Reach

 * In Halo: The Fall of Reach, Aki Hikowa and Ellen Dowski are female officers of the Pillar of Autumn. However, on the level The Pillar of Autumn, the bridge has no female members.
 * This may imply that, like modern navy ships, the Autumn has rotating shifts. The obvious Doylist explanation is that no female crew members were modeled.


 * William Lovell's eyes are stated to be green in Halo: The Fall of Reach, but in Halo: Combat Evolved, the Autumn's crew has no green-eyed members.
 * This is likely a result of game engine limitations, or due to rotating shifts, Lovell was simply not present on the bridge at the time.


 * In Halo: The Fall of Reach, the description of the Pillar of Autumn is considerably different from its Halo: Combat Evolved incarnation. The bridge is described as having a command chair and a curved viewport; in Halo: Combat Evolved, this chair is absent and the window consists of several flat sections. The novel also describes the bridge as being extremely cramped, with only a meter of space between the command chair and the other stations, while in the game, the bridge is clearly more spacious. According to the novel, there is also an elevator leading directly from the engine room to the bridge. In the game, the engineering and the bridge are on the same level, and there are no doors which may belong to an elevator adjoining the bridge. In addition, the engine room is described as being "hexagonal", while in the game, it consists of two vaguely rectangular chambers with the engine core in the middle. In the Combat Evolved level The Maw, it is stated that the Pillar of Autumn has four fusion reactors, each of which is destroyed by the player; in The Fall of Reach, the ship is also said to have a single main reactor nestled within two smaller reactor rings. The ship is also described as having rotating centrifuges to generate artificial gravity; no rotating sections are present in the game, unless they are located within the hull.


 * In Halo: The Fall of Reach, when Captain Keyes awakens from cryo, Cortana informs him that the capacitors of the Pillar of Autumn's MAC gun are depolarized and the gun cannot fire, yet the gun is apparently used, and the loss of fire control is treated as a significant piece of dialogue in Halo: Combat Evolved's opening cutscene.
 * It is possible that the crew managed to get the gun working again before the battle.

Halo: Combat Evolved manual

 * The Halo: Combat Evolved manual states that the Harvest incident took place in 2520, while all other sources specify 2525.
 * The manual also states that Captain Keyes has served in the UNSC since 2526, though The Fall of Reach clearly states that he was fresh out of OCS in 2517.
 * The Grunts are referred to as being five feet tall in the Halo: Combat Evolved manual, but in The Fall of Reach, they are referred to as being a meter tall (just over three feet). Although it could be that Grunts are "a meter tall" in a natural combat stance, while they are actually "five feet tall" if they stand up straight, without a methane tank attached to their backs.
 * According to the manual, the Covenant attacked Reach two days before the Spartans' mission to capture a Prophet was to begin. This is contradicted in Halo: The Fall of Reach and First Strike, in both of which the Pillar of Autumn is already departing for the mission when the Covenant attack.
 * The manual refers to the as a colony ship. The ship is said to be a frigate in Halo: The Fall of Reach.

Halo: The Flood

 * In Halo: The Fall of Reach, Lieutenants Hall and Dominique are introduced as members of the command crew of the Pillar of Autumn, but are absent in Halo: The Flood when the ship arrives at Installation 04.


 * On page 3 of Halo: The Flood, Thom Shephard tells Sam Marcus that they are resuscitating John-117 before the Pillar of Autumn exits Slipspace. However, in Halo: Combat Evolved, it is clearly shown that Captain Keyes orders that John-117 be taken out of cryo after the Autumn is seen drifting in space and is preparing to be overrun by the Covenant.


 * In Halo: The Flood, the presence of the Covenant at Installation 04 is regarded as being unrelated to the arrival of the Pillar of Autumn; the Covenant are surprised by the arrival of the human ship and act as if it ended up in the system by either following one of their ships, or by chance. However, Halo: Combat Evolved, Halo 2 and the Covenant broadcast log featured in the Adjunct section in the 2010 reissue on The Flood, state that the Covenant found the ring specifically by following the Autumn's slipspace jump from Reach, and arrived at the system in advance, waiting for the Autumn on the far side of Threshold.


 * In Halo: The Flood, Captain Keyes comments that a single plasma torpedo is capable of destroying the Pillar of Autumn, though in Halo: Combat Evolved it is struck by several without losing structural integrity and breaking up.
 * This possibly relates to the Minor Prophet's order to not fire plasma torpedoes. Additionally, the Covenant ships may have chosen to fire undercharged shots to minimize damage to Halo caused by stray shots.


 * In Halo: The Flood, Cortana identifies Installation 04 as "Halo" in Halo: The Flood when escaping the Pillar of Autumn, but in Halo: Combat Evolved, it is not identified by this name until the level Truth and Reconciliation, when Captain Keyes mentions overhearing the name from his Covenant captors.


 * According to Halo: The Flood, there was an ocean at the bottom of the desert plateau the Truth and Reconciliation was holding position on. However, in both Halo: Combat Evolved and Halo: Combat Evolved Anniversary, there is only solid ground below the plateau.


 * In the Halo: Combat Evolved level Halo, Cortana mentions that the survivors rescued by John-117 would be transported to the "command shuttle". The command shuttle is not mentioned in Halo: The Flood, where Alpha Base serves as the main command post for UNSC forces.


 * In Halo: Combat Evolved, Cortana accesses Installation 04's Control Center by having the Master Chief remove her memory chip from his helmet and place it in the console. In Halo: The Flood, she broadcasts herself into the system using the suit's transmitter.


 * There are several differences between Halo: The Flood and the Halo: Combat Evolved level The Maw in the encounter at the final service elevator on the Pillar of Autumn. In Halo: The Flood, Zuka 'Zamamee confronts John-117 by using a Shade turret, accompanied by several Grunts. Cortana takes control of the elevator and causes it to descend, allowing John-117 to drop in a pair of grenades and take out the Covenant. In the game, there are two Special Operations Elites on the elevator and no Shade turret. In addition, Cortana does not move the elevator.


 * In Halo: The Flood, many of the Marines John-117 fought alongside were female, despite no female Marines being in Halo: Combat Evolved at all.


 * In Halo: The Flood, Sergeant Stacker is not mentioned at any point, despite him being present on several occasions in the game. He is replaced during the raid on the Truth and Reconciliation by Sergeant Parker, and for the raid on the Silent Cartographer by Gunnery Sergeant Waller. One place where he might make an appearance is when the Chief rescued a crashed Marine squad with an unnamed Sergeant, where Stacker is normally found in the game.


 * Throughout Halo: The Flood, the Master Chief's or other characters' weapon loadouts at a given situation occasionally differ from those in the game. Stocks of ammo left behind by dead marines are not mentioned either.
 * In Chapter 4, during the raid on the Truth and Reconciliation, the novel illustrates that John ran out of ammo for his MA5B Assault Rifle, switching to an M6D pistol; in the game, there are no pistols on that level at all.
 * Also in Chapter 4, it is stated that "the Spartan was carrying a full combat load of ammo, grenades, and other gear, plus two magazines for the M19 launchers". In the game, the Master Chief was not carrying a rocket launcher nor any magazines for it at the time.
 * The novel consistently describes Marines wielding rocket launchers; no marines are ever seen wielding rocket launchers in the game.
 * This is due to in-game constraints, as is the inability for marines to drive Warthogs.


 * As revealed in later sources, the Covenant has revered Forerunner AIs as "Oracles" for a long time, but in Halo: The Flood, 343 Guilty Spark was regarded as an enemy by the Sangheili.
 * This is probably because the fiction regarding the Covenant's beliefs had not yet been cemented by the time The Flood was written.

Halo: First Strike

 * In Halo: Combat Evolved, the Master Chief throws Private Jenkins' recorder chip away, but he still has it in First Strike. This could be explained by the Chief's suit automatically making a copy of Jenkins' recording as a possible means of gathering intelligence, although this is only a theory.


 * It is stated in Halo: First Strike that Dr. Halsey always referred to John by name, and never by rank or serial number. However, in Halo: The Fall of Reach, she called him "Master Chief" repeatedly.


 * During Chapter 33 of Halo: The Fall of Reach, many Covenant ships are destroyed, but not before they can let loose their plasma torpedoes which then destroy UNSC orbital defense platforms. However, during a space battle in Halo: First Strike, plasma en route to a target merely dissipates as the originating ship and its magnetic controls are destroyed. It is possible that the magnetic controls were not destroyed in the former instance, allowing the plasma to continue to its target.

Halo: Ghosts of Onyx

 * The frigate is erroneously referred to as a destroyer.


 * In Halo: First Strike, Dr. Halsey puts four submachine guns in a bag. In Halo: Ghosts of Onyx, Kelly found the same weapons, but they were four MA5B Assault Rifles instead.


 * In Halo: Ghosts of Onyx, Kurt Ambrose remarks that some of the Alpha Company candidates were orphaned at Jericho VII. His speech takes place on December 12, 2531, yet Jericho VII was not glassed until February 2535.
 * While this is most likely to be a simple oversight, it is possible that the candidates from Jericho VII were orphaned in a yet-unseen engagement that preceded the Covenant attack of 2535, as the background of the Covenant invasion of Jericho VII is not elaborated upon in The Fall of Reach. For example, the events that occurred may have been similar to how the Covenant initially invaded Arcadia in 2531 but only arrived to glass the planet eighteen years later.


 * On page 129 of Halo: Ghosts of Onyx, Franklin Mendez was mentioned to be "pushing sixty [years old]", which implies that his birthdate is close to or after 2493. However, this would give him a maximum age of 24 when he started training the SPARTAN-IIs, which is unlikely given his description of "grey hair at the temples" and "having seen much combat" as well as his high rank of Chief Petty Officer. In Halo: Glasslands, Mendez is mentioned as being the same age as Dr. Halsey, who is sixty at the time.

Halo: Contact Harvest

 * Halo: The Fall of Reach states that Harvest has a population of three million. However, in Halo: Contact Harvest, it is stated to have a little over 300,000. The figure presented in Contact Harvest has been ignored in later media, and the population is listed as three million in Halo: Fall of Reach - Boot Camp and Halo: The Essential Visual Guide.


 * Throughout Halo: Contact Harvest, the Eridanus and Epsilon Eridani star systems are referenced as being one system: "Epsilon Eridanus". It is implied that both Reach and Eridanus II are situated in this system. With two exceptions, (a chapter heading in the first printing of Halo: The Fall of Reach and the "Reclaimer" entry in the Bestiarum), the two systems are regarded as separate in all other fiction; in Halo: First Strike, for instance, the main characters travel from Epsilon Eridani to Eridanus, a journey that would take days were it not for the Forerunner crystal from beneath CASTLE Base.


 * The Insurrection is described as being largely confined to the aforementioned "Epsilon Eridanus" system, whereas outer systems are described as being more stable due to their more homogeneous populaces. In other media, the Insurrection is depicted as occurring almost exclusively in the Outer Colonies and spanning numerous star systems. Additionally, the highly varied populations of the Outer Colonies are cited as one of the reasons for their instability. Prior to Contact Harvest, no mention was made of fighting breaking out in Epsilon Eridani; on the other hand, the conflict was described as being at its most active in the similarly named Eridanus system. This has been partly reconciled in later fiction, with the Insurrection being active in both systems, although the claim that the conflict at large was confined to Eridanus has been ignored.


 * In Halo: Contact Harvest, humanity is said to have seventeen planetary colonies. In a forum post, Joseph Staten suggested that a large number of the colonies are smaller settlements or outposts; he admitted to being "intentionally vague" in order to leave room for possible future expansion. Later media, (as well as the pre-release Halo: Combat Evolved timeline), have ignored Staten's claim, showing that the Unified Earth Government had, at the very least, several dozen developed colony planets and had some presence on over 800 worlds.

Halo: The Cole Protocol

 * In Halo: The Flood it says Captain Keyes killed his first human with a pistol, which was specifically stated to have a barrel; however, Halo: The Cole Protocol states he used a modified plasma rifle, a weapon which lacks any form of barrel.


 * Thel 'Vadam reacts to Jai-006's face-concealing MJOLNIR helmet with extreme disgust, believing that only a "soulless and dead" being would hide his face. This is contradictory in light of the fact that many Sangheili combat harness variants have helmets that fully cover the wearer's face.

Halo Wars

 * Although the Forerunner relic on Harvest is discussed by Captain Cutter and Professor Anders at the end of Halo Wars: Genesis, its discovery is treated as new information in the game's opening cinematic. The simplest explanation is that Forge's discovery of the relic in the cutscene takes place during the events of Genesis.
 * In all renders and cutscenes, most notably "She Is Not My Girlfriend" at the beginning of the level Anders' Signal, the M41 Light Anti-Aircraft Gun is shown with four barrels. It is likely that this is a variant of the M41 LAAG, similar in design to the M41 Extended Light Anti-Aircraft Gun mounted on the OF-92 Booster Frame.

Halo 3: ODST

 * The depiction of the city of New Mombasa in Halo 3: ODST differs significantly from its Halo 2 incarnation, the most prominent changes being the replacement of the Mombasa Tether to a separate island and a major restructuring of the island's general shape. As a result, the Prophet of Regret's assault carrier Solemn Penance is also moved to a different location over the city than it was in Halo 2.


 * In Halo 3: ODST, the Solemn Penance is seen as being stationary just prior to it jumping into slipspace, yet in Halo 2 during the closing cutscene of the level Metropolis, the assault carrier is moving forward.
 * During the same scene in Halo 3: ODST, the In Amber Clad is seen approaching the carrier in a straight line and is clearly separate when they jump, but in Halo 2, the In Amber Clad flies in an arc to a position underneath the starboard side of the assault carrier. These changes were made for the sake of drama and to make the scene easier to witness from the Rookie's point of view.


 * In the profiles for the members of Buck's squad, it is shown that Kojo Agu enlisted in the UNSC when he was only 17 years old, after serving as a merchant marine. As shown in i love bees and later Halo: Glasslands, the minimum age of enlistment for the UNSC is 18 years.
 * It can be assumed that an exception was made for Agu, as it is noted he was retained on service for actions that normally would get a trooper discharged. Additionally it is possible the recruiters overlooked his age given the fact humanity was at war with the Covenant and needed as many recruits as possible.
 * Likewise, considering Agu's personality, he could also have lied about his age.


 * Some of the dead Sangheili corpses found around New Mombasa are wearing the Assault harness, even though they were killed just before the Great Schism and the Assault harness was banned from use until after the Sangheili seceded from the Covenant.

Halo: Evolutions - Essential Tales of the Halo Universe

 * In The Mona Lisa, it is repeatedly stated that the UNSC had a "policy" not to take Covenant prisoners and the main characters are shown to be baffled about discovering Covenant prisoners aboard the prison vessel Mona Lisa. However, UNSC personnel are shown taking Covenant prisoners in Halo: The Flood, Halo Wars: Genesis, and several later sources. It is likely that the "policy" to which the characters refer is a guideline or standard operating procedure rather than a official, strictly enforced protocol.


 * The specifics of the events of the ground battle in New Mombasa differ significantly between the Halo 2 level Metropolis and the Halo: Evolutions story Palace Hotel. In addition to extensive changes in dialog, several events and locations are described differently. For example, the scene in the parking lot of the Kilindini Park Cultural Center, featured in Palace Hotel, is not present in the game. The ending of Palace Hotel is also different from Metropolis, where John makes his way to a Marine outpost in a corporate building instead of a hotel. In the game, it is mentioned that the Marines' lieutenant was killed as soon as they arrived and that Sergeant Banks is in charge at the time, while in Palace Hotel, John meets the Marines' lieutenant at the outpost. Overall, Palace Hotel could be regarded as an alternate-continuity take on the story as presented in Halo 2, much as the Fall of Reach comic series is an alternate incarnation of the novel's story.


 * In Human Weakness, Cortana knows about the death of Colonel James Ackerson while being held captive by the Gravemind in High Charity. There is no way she could possibly have been aware of the event at this point, as Ackerson was killed after the Battle of Cleveland sometime between November 8 and 17, and the scene in High Charity takes place days prior. Even accounting for the possibility she may have somehow learned this immediately after Ackerson was executed, she refers to the event in a fashion as if she had been aware of it beforehand.


 * In The Impossible Life and the Possible Death of Preston J. Cole, it is clearly stated that Vice Admiral Preston Cole had 117 ships under his command during the Battle of Alpha Aurigae. Halo Wars: Genesis states he had only 107 ships in the same battle. The revised number is an obvious reference to John-117, so it could be considered an Easter egg.


 * According to The Impossible Life and the Possible Death of Preston J. Cole, two of Preston Cole's grandfathers served in the Rain Forest Wars. This seems unlikely, as the conflict took place over three centuries before Cole's birth.


 * In Halo Wars: Genesis, the Halo Wars in-game timeline, and the pre-release timeline for Halo: Combat Evolved, Preston Cole is said to have been promoted to full admiral after his victory at Harvest. In The Impossible Life and the Possible Death of Preston J. Cole, no mention is made of his promotion and he is referred to as a vice admiral throughout the story, even as late as his final broadcast in the Battle of Psi Serpentis in 2543; Halo: The Essential Visual Guide also refers to him as a vice admiral. It is possible his rank expired or he may have been demoted in an unseen event. Nonetheless, the ONI memorial in Halo 3: ODST refers to him posthumously as a full admiral.


 * In The Impossible Life and the Possible Death of Preston J. Cole, the CCS-class battlecruiser is said to have first been encountered at the Battle of Psi Serpentis in 2543. This contradicts Halo Wars: Genesis, which shows Cole's fleet engaging such vessels in 2526; Halo Wars, in which two CCS-class ships are encountered and identified by class at Arcadia in 2531; data pad 10, which states that the Assembly's findings about glassing were derived from observing the CCS class in 2526; and Halo: The Essential Visual Guide and the Halo Encyclopedia, which state that vessels of the class were encountered frequently throughout the war.


 * In The Impossible Life and the Possible Death of Preston J. Cole, Admiral Cole states in reference to the Reach super-AI network that "They're the only ones in the Outer Colonies with the raw power to get the job done," despite Reach being part of the Inner Colonies.

Halo: Reach

 * In Halo: Combat Evolved, as well as Halo: The Flood, which take place directly after Halo: Reach, the Marines on board the Pillar of Autumn are armed with MA5B assault rifles. However, in Reach, the Marines assigned to the Pillar of Autumn are armed with MA37 assault rifles.
 * From a game design perspective, this is due to Bungie declining to spend resources to create a weapon that would already have its place in the "sandbox" filled, especially given the relatively brief appearance it would make. From a canon perspective, it has since been explained that Marines will utilize Army weaponry should the situation require, as occurs in Halo: Reach.


 * According to an Intersystem News sheet that comes with the Limited and Legendary editions of the game, Jacob Keyes was already a captain in 2550. However, according to Halo: The Fall of Reach, he was not promoted to captain until after he performed the famous Keyes Loop in July 2552.


 * The placement of the multiplayer map Breakneck in New Mombasa is inconsistent with the city's Halo 3: ODST incarnation. Assuming the locations of the city's landmarks, such as the bridge of the Uplift Reserve, are consistent with ODST, the map should be situated near the southernmost main section of the Reserve. No skyscrapers or streets are present in the area in ODST. In addition, according to the player's HUD compass, the city center and the Mombasa tether are situated to the south and southwest of the map, respectively. Based on the way the city is presented in ODST, the aforementioned landmarks would be located to the north and northwest of the Uplift Reserve and thus the map's playable area.

Halo: Glasslands

 * At the conclusion of Halo: Ghosts of Onyx, Onyx dissolves into trillions of Onyx Sentinels that vaporize any vessels nearby and remain to guard the slipspace rift to the shield world formerly in the core of the planet. These Sentinels are wholly absent in Glasslands, in which UNSC vessels are capable of traversing the former site of Onyx, now said to contain a debris field, without any sign of threat. While the Onyx Sentinels are mentioned in passing when referencing past events, their apparent disappearance is never noted nor addressed.


 * Lieutenant Commander Kurt Ambrose is referred to as "Lieutenant" Ambrose.


 * During one of her briefings to Kilo-Five, Serin Osman operates under the presumption that the existence of Onyx, as well as Parangosky's cover-up of the planet, would be common knowledge. The planet was removed from all navigation charts and databases in 2511, before most members of Kilo-Five were born. As such, the rest of Kilo-Five, apart from Osman and Black-Box, would have no way of knowing that a planet called Onyx existed in the first place, much less that Parangosky classified it. While it is possible that some information about the planet did leak out to the public (as suggested in Halo Wars: Genesis), Osman's assumption that non-regular ONI personnel would be familiar with a single, obscure planet among humanity's hundreds of colonies is highly doubtful.


 * Captain Osman claims that the UNSC had captured and defused a Huragok "a couple of years ago", and that ONI made several technological developments by reverse-engineering the data it contained. She implies that the Engineer had died and states that ONI needs more than one Huragok so they can repair each other and reproduce. Strangely, she does not mention that several Huragok were rounded up aboard the when it returned to Earth, nor does she say that one was rescued from New Mombasa and interrogated shortly thereafter. It is possible that she refrained from telling the "whole truth" to motivate her team to board Piety and capture the Engineer onboard.


 * It is implied that Halsey threatened someone with her personal sidearm when hijacking the Beatrice; this is used as basis by CPO Mendez for confiscating her pistol. Halo: First Strike describes the event in question, and no threats are involved when Halsey boards the vessel - empty at the time - and leaves unopposed. Additionally, Mendez refers to the incident as if he had been present, even though he did not have first-hand knowledge that Halsey had stolen a ship in the first place; him knowing about the event would be based on Blue Team's, or Halsey's own, accounts.


 * According to Halo: Glasslands, Dr. Halsey did not have an AI to help her decipher Forerunner symbols while in the shield world. However, she had the "micro" AI Jerrod in her laptop in Halo: Ghosts of Onyx, helping her translate Forerunner symbols while they traversed the interior of Onyx. No mention was made of Halsey losing Jerrod, and she still had her laptop after she and the other survivors had entered the shield world.


 * During an argument with Dr. Halsey, CPO Mendez claims that the SPARTAN-III program lacked any form of genetic filtering. In Halo: Ghosts of Onyx, Mendez is personally present at a meeting where it is established that the SPARTAN-III program did indeed have a set of genetic qualifications, a necessity because the biochemical augmentations at the time were only compatible with a particular series of genetic markers, and any deviations would carry a significantly increased risk of failure. For this reason, the initial pool of candidates for Beta Company had to be reduced from the original projection of nearly one thousand to 375.


 * Lucy-B091 lashes out in a fit of rage and strikes Dr. Halsey in the face with strength enough to "send a shock wave right up her arm" and leave her hand "throbbing". Halsey quickly recovers and does not suffer more apparent injury than a slightly bleeding nose. Based on prior evidence of the SPARTAN-IIIs' physical strength, combined with the SPI armor's hardened gauntlet plating, such a blow would have inevitably resulted in Halsey's death. SPARTAN-IIIs have been stated to possess the strength of "three normal soldiers", and while Lucy is around twenty at the time, SPARTAN-IIIs have been described as being capable of matching Sangheili and other Covenant in close-quarters at only twelve years of age, effortlessly snapping the aliens' necks and limbs, demonstrating strength that would certainly be lethal against a frail, aging human.


 * When the survivors in the shield world reestablish contact with the UNSC, Admiral Parangosky tells Dr. Halsey that it has been "five months" since John-117 and Cortana went missing after stopping the Halo Array from firing. However, John and Cortana disappeared on December 11, 2552, with the UNSC receiving confirmation of this when the Arbiter returned to Earth on December 23. The scene with Parangosky informing Halsey about their disappearance occurs in February 2553, so less than three months had passed at that point. Even considering the possibility that Parangosky may have lied, she would have no reason to do so, as both she and Halsey were aware of a transmission sent by Cortana on November 3 - less than four months earlier - in which she announced that John was on his way to Earth.


 * Glasslands maintains that Dr. Halsey attempted to hide the SPARTAN-II flash clone replacement operation from the upper echelons of ONI; Admiral Parangosky claims that she did not learn about the clones until years afterward. When referenced in previous fiction, the flash cloning operation is never singled out as something separate or particularly secretive in comparison to all other aspects of the program; on the contrary, ONI is unanimously identified as the chiefly responsible party as opposed to Halsey alone. In Halo: The Fall of Reach, John-117's classified file, accessed by Cortana, refers to the replacement operation as an "ONI black op". In Halo: First Strike, Halsey refers to the "old flash clone techniques that ONI had used to replace the originals". In her journal, Halsey refers to the clones like any other part of the program, failing to mention any attempt to conceal it. Furthermore, Halo: First Strike notes that Colonel James Ackerson had the clones monitored as they grew up and even had the bodies retrieved after they died, which calls into question Parangosky's statements of not learning about the cloning operation until years later. It is also suspect that Halsey would see it necessary to conceal this particular aspect of the program from ONI, given their oft-demonstrated neglect for moral concerns, particularly where the secrecy of their operations is concerned. Had there been an attempt to withhold information, it would have been futile from the beginning; the dozens of ONI scientists and field agents that carried out the operation would have relayed the information to ONI's leadership, provided that the ONI surveillance of the program failed to do so.

Halo: The Thursday War

 * The carries a large arsenal of nuclear weapons onboard and is yet capable of remaining completely undetected over Sanghelios. According to Halo: Ghosts of Onyx, this would be impossible, as the plutonium in nuclear weapons negates any stealth measures upon slipspace transition by emitting an easily detectable Čerenkov radiation signature, forcing even stealth vessels to jettison any onboard nukes in order to perform a cloaked slipspace exit. However, Port Stanley had been heavily upgraded with Forerunner technology, so it is possible that this flaw had been alleviated.


 * Dr. Catherine Halsey is portrayed as being entirely unfamiliar with the concept of a fourth-generation AI and appears to believe Black-Box when he falsely claims that fourth-generation AIs are created by other AIs. However, in Halo: Ghosts of Onyx, Halsey demonstrates close familiarity with fifth-generation smart AIs and has an intimate understanding of their behavior; she is able use a Zen koan to attract the attention of Endless Summer and states that fifth-generation smart AIs like to "show off".
 * It is possible that Halsey feigned ignorance out of unwillingness to help Admiral Parangosky's underlings, who were responsible for her arrest and regarded her with open contempt. However, Black-Box would most likely have known the full extent of her expertise given his unrestricted access to her and ONI's files, but he appears to regard Halsey's ignorance about the development of fourth-generation AIs such as himself as a fact.


 * While on Trevelyan, Jul 'Mdama is said to be able to determine the passage of time based on the "position of the sun". Given the structure's nature as a full-size Dyson shell, this would be impossible, as the sun would always be directly overhead any point on the sphere's interior surface.


 * The Sangheili are revealed to have an insult for humans: "nishum", which roughly means "intestinal parasite". The name is derived from the Sangheili mistaking armored humans for creatures with exoskeletons, then after examining dead human bodies concluding that they are parasites inside insectoid beasts. However, the Sangheili themselves wear body armor (which is often thicker and more carapace-like in design than standard human infantry armor), as do most of the Covenant species, so it seems suspect of them to not be able tell that humans wear artificial armor just like they do.


 * Dr. Halsey asks Black-Box "So which ship or Spartan are you assigned to?" upon encountering the AI. This question is absurd in the given context, as it excludes a broad range of assignments in which AIs are commonly known to serve, while equating Spartans with ships as one of two noteworthy posts for AIs; Halsey would have no reason to presume that an AI would be assigned to a Spartan, given that Cortana's assignment to John-117 was a one-time exception and not a standard procedure among Spartans.

Halo 4: Forward Unto Dawn

 * Cygnus, Chyler Silva's birthplace, is described as a center of violent Insurrection activity. According to Halo: Contact Harvest, the Cygnus system had not been involved in the Insurrection as of 2524.
 * In Halo 4, it is implied that coordinate data from an incident with a Forerunner artifact at Installation 03 led the UNSC Infinity to Requiem. No mention is made of the Infinity picking up Cortana's distress call which results in the ship and its battle group making a slipspace jump toward Requiem in Halo 4: Forward Unto Dawn. Although the Infinity receives the distress call in Halo 4, this appears to be after the ship is already near Requiem; in Forward Unto Dawn, the signal is picked up while the Infinity is still light-years away, as evidenced by the crew having to enter cryo-sleep for the journey.
 * Forward Unto Dawn also depicts a considerably different interpretation of Cortana's introduction as depicted in the game. In the game her avatar simply winks into existence when intruders are detected aboard the ship; she then calmly (though hesitantly) revives John with the words, "Wake up, Chief. I need you." In the webseries, however, Cortana experiences a series of violent personality shifts (at one point vowing to let John die with her) until the Dawn ' s sensors detect Requiem. Cortana's avatar then dramatically fades from a large sphere to a much smaller point, from which she then appears. She then wordlessly begins thawing the Master Chief's cryo chamber without using the holographic terminal seen in the game. In the level Dawn Cortana claims to be unaware of the ship's proximity to Requiem; however, she should have been able to see it through her neural link with John, so she was likely either joking or experiencing the effects of rampancy.
 * Halo 4: Forward Unto Dawn depicts a fleet of more than two dozen cruisers and frigates accompanying Infinity to Requiem. The Commissioning shows only two s by the time Infinity has reached Requiem, though the camera angle obscures any other ships that may be present. Regardless, this escort fleet is never mentioned in the game.
 * The fleet may have been sent to deal with the Covenant ships still in orbit above Requiem. However, the fleet is never mentioned during the level Shutdown, when it could have been used to intercept Mantle's Approach before the Didact could escape Requiem.
 * At the end of the webseries, most ships in the fleet are shown entering slipspace under their own power. However, some of the vessels hold formation so closely to Infinity that they may have entered its slipspace rupture and followed its wake; the two closest frigates maintain the same formation as those seen in The Commissioning. It is possible that these ships arrived alongside Infinity while the rest of the ships were outpaced due to their slower engines, thus explaining the frigates seen in the trailer. They may have been destroyed when Requiem began pulling the flagship inside, explaining the high volume of debris seen cascading toward the shield world.

Scanned
Linda-058 and two other female Spartans are portrayed with long hair during the augmentation procedures. According to Halo: The Fall of Reach, all of the Spartans had their heads shaved in preparation for the procedure.

Halo 4

 * In the Prologue cutscene, many inconsistencies are shown. It is implied that Halsey is imagining most of the cinematic's visuals.
 * While the Spartans seem to be wearing John-117's uniquely upgraded armor, Halo 4: The Essential Visual Guide retcons these suits into the Mark IV variant upon which John's suit was based. They are still depicted with energy shields, though MJOLNIR energy shield tests had begun as early as 2531.
 * In John-117's accessible service record in the level Dawn, the Pillar of Autumn is misidentified as a frigate.
 * Although Cortana used nanomachines to heavily overhaul John's armor while he was in cryo, the suit retains a gash on its right side received from John's freefall drop in Halo 3.
 * Since John's full armor is never seen until the opening cutscene of the level Requiem, it is possible that the gash was indeed repaired only for the suit to be damaged again after John fell into the shield world.
 * Despite maintaining a generally similar profile, Halo 4 ' s incarnation of Forward Unto Dawn is noticeably different from its appearance in Halo 3. The ship appears much larger, with more of the forward half remaining intact, though the ship is still canonically 490 meters long. The number of engines has been reduced; rather than having two primaries on the main hull and two secondaries on the "wings", there are only two primary engines. The port and starboard hangar bays have been reduced from five small bays on either side to one much larger bay on either side; they are moved much farther back, remaining with the aft section. The enlarged cargo bay, a defining feature of the Charon class, is conspicuously absent or is at least moved inside the hull; either way, this creates an inconsistency with the final cutscene of the level Halo. The point defense guns have been retconned into two separate models, increased in number, and moved to different areas on the hull. The ship's cryo tubes have also been remodeled and the cryo bay has been rearranged.
 * From a production standpoint, the ship was enlarged to create a more dynamic and exciting playspace; the original model would have been very small and cramped, limiting the first level's gameplay potential. The more superficial changes, such as those made to the cryo tubes and the point defense guns, are intended to reflect Halo 4's revamped art style.
 * The Cryptum that preserved the Didact on Erde-Tyrene left him very weak, and he had to be reinvigorated through a nutrient bath to regain his strength, a process that took several days. In Halo 4, the Didact's Cryptum has preserved him perfectly for over a hundred millennia and he has not suffered any kind of muscle loss.
 * According to Halo: Silentium, the Cryptum the Librarian imprisoned the Didact in is a "combat Cryptum", though the nature of this variant is never elaborated upon.
 * The Didact, in both his forms, is depicted with thick, spike-like protrusions in the place of hair; he is described as having a patch of pale, bluish white fur as in The Forerunner Saga.
 * Slipspace is described as an entirely featureless, pitch-black void in most previous media, a direct result of its inherently "nonvisible" nature.   In the level Midnight, though, slipspace resembles a bluish expanse with white streaks of stars being flown past. Likewise in the opening cutscene of Departure slipspace appears as a kaleidoscope of colors. This may be from both ships using Forerunner slipspace engines, which have been observed to create differing environments.
 * The terminals introduce many incongruities with The Forerunner Saga. However, 343 Industries has clarified that the terminals are a condensed version of the more complex story in the novels and should not be taken as a literal account; in-universe, this is explained with the unreliability of the Domain, through which the terminal records are presented.

Halo: Initiation

 * The first issue of Halo: Initiation references Sarah Palmer as a lance corporal, and later corporal, during her ODST career immediately prior to her recruitment into the SPARTAN-IV program. According to Palmer's biography on the official Halo 4 website, she spent much of her Marine career as a lieutenant. Additionally, Captain Del Rio calls Palmer a lieutenant when ordering her to apprehend John-117 in the Halo 4 level Reclaimer. Halo 4: The Essential Visual Guide states that Palmer's leadership skill was the primary reason for her selection as a Spartan; assuming Palmer was a lance corporal, it is unlikely that such qualities could even be ascertained in practice, as a lance corporal would have virtually no command experience.

Halo: Mortal Dictata

 * According to a video clip of the early days of SPARTAN-II indoctrination shown to Naomi-010 by Black-Box, Dr. Halsey lied to Naomi that her father had approved of her conscription and was not expecting her to return home. In Halo: The Fall of Reach, Halsey specifically states, contrary to Déjà's recommendations, that they will not attempt to lie to the children about their parents to motivate them out of risk that the Spartans may go rogue if they ever learned the truth.
 * Given that the recordings also show the children exhibiting more extreme reactions to their abduction than Dr. Halsey's observes in her journal, it is possible that ONI tampered with the records to make Halsey's part in the program look more morally reprehensible as part of their campaign to smear her reputation; or, more specifically, to manipulate Naomi in particular.


 * The SPARTAN-II candidate abduction process is depicted with several incongruities. Retrieval team Theta 2 is shown to first kidnap Naomi-010 and transfer her clothes to the flash clone, which is only then released—several kilometers distant from the spot where she was originally taken—but not before Naomi temporarily escapes, leading to the whole replacement operation lasting several hours. This drives her family to panic about her disappearance and an extensive search operation is organized before she is "found". The need for the clothing transfer procedure is questionable, given that Halo: Fall of Reach and Scanned depict the clones wearing duplicate clothing, enabling ONI to switch the children on site and thus removing the need for a potentially suspicious disappearance before the clone is returned.


 * Plasma torpedoes aboard Pious Inquisitor are referenced as physical munitions stored in a dedicated "torpedo bay". In previous fiction, plasma torpedoes have been established as shaped agglomerations of electromagnetically-guided plasma, not unlike the bolts fired by handheld plasma weapons. The "torpedoes" are brought into existence at the time the weapon fires and do not exist in any meaningful capacity aboard the vessel.
 * The references to "plasma torpedoes" can be interpreted as referring to the ship's supply of superheated plasma used to generate the torpedoes, although the wording used suggests that the torpedoes themselves are stored onboard the ship.

Ancillary material

 * In Halo: Ghosts of Onyx, Frederic-104 is promoted to the rank of Lieutenant, Junior Grade near the end of the Battle of Onyx. However, the interrogation transcript featured in the Adjunct section of the 2010 edition of Halo: First Strike continuously refers to him as a lieutenant by the start of the Battle of Earth.


 * The ONI Directorate Memorandum Interrogation Findings log included in the Adjunct section of the 2010 edition of Halo: The Fall of Reach refers to Preston Cole as a fleet admiral. Though there is a conflict over Cole's rank between Halo Wars: Genesis and The Impossible Life and Death of Preston J. Cole (see here), no other source has referred to him as a fleet admiral.

Several sources
Conflicts which involve more than two sources are listed here.


 * All pertinent media released since 2009 state that 25 of the 28 active SPARTAN-IIs were summoned to Reach for Operation: RED FLAG. All sources agree that 33 SPARTAN-IIs successfully adapted to the augmentations. Three Spartans were killed in action and one was too wounded to continue active duty in the decade between 2542 and August 29, 2552. Kurt-051 and Randall-037 were listed as missing in 2531; the former was kidnapped by ONI to lead the SPARTAN-III program, while the latter was most likely killed in action, though Dr. Halsey considered him to be truly MIA. During the same year, Douglas-042, Jerome-092, and Alice-130 became stranded outside UEG space, unable to contact allied forces, and were declared MIA in 2534. Jai-006, Adriana-111, and Mike-120 had been missing since 2551. SPARTAN-IIs confirmed KIA prior to the Fall of Reach include Samuel-034, Daisy-023, Sheila-065, Solomon-069, and Arthur-079;  Cal-141 is obviously meant to have died, though her death contradicts the statement that only three SPARTAN-IIs were killed between 2542 and 2552. Jorge-052 fought during the Fall of Reach, though he served with Army SPECWAR's NOBLE Team rather than being recalled for Operation: RED FLAG. The Kilo-Five Trilogy makes no mention of Naomi-010's participation (or lack thereof) during the invasion of Reach; if she did fight on Reach the means for her survival are unclear. By this count, no more than 18 SPARTAN-IIs could have been present for Operation: RED FLAG, with Naomi's potential absence reducing the number to 17.
 * In her journal, Dr. Catherine Halsey expressed her hope that Kirk-018 and René-081, two of the twelve crippled "washouts", could be rehabilitated and returned to active duty. Soren-066 escaped the program in 2526, having unwittingly joined the Insurrectionist cause; Halsey refused to bring him back into the fold against his will and he presumably died soon afterward. Ralph-303 was discharged due to psychological problems and his augmentations were curtailed; he later joined the Marine Corps and died in 2531. Serin-019 was reassigned to the Office of Naval Intelligence as CINCONI Margaret Parangosky's personal attache, while the wheelchair-bound Fhajad-084 became an ONI data analyst. Maria-062 became the only Spartan to retire after washing out of the program, though she was still capable of wearing MJOLNIR armor as of October 2552. Cassandra-075 was still undergoing skin grafts as of October 2552. Musa-096 also became wheelchair-bound and, by January 2553, was responsible for developing the SPARTAN-IV Program. Including Kirk and René, this leaves five washouts who were potentially rehabilitated and returned to active duty, which could increase the number of Spartans at Reach to as many as 23.
 * Dr. Halsey refused to allow invasive autopsies on the deceased Spartan candidates' bodies and arranged a closed-casket funeral; the coffins were empty and the bodies were actually placed in cryonic storage. She feared what ONI would do with the candidates' cadavers, suspecting that they would form their own, secret Spartan unit. Given that Halsey resurrected Linda-058 from clinical death with the rather limited facilities aboard the, it is possible, though very unlikely, that the SPARTAN-IIs' numbers were bolstered by some of their once-clinically deceased comrades.
 * Yasmine Zaman was conscripted as part of the second class of the SPARTAN-II program. Although she died, Nicole-458 was successfully augmented and it is possible others were and bolstered the ranks of the depleted SPARTAN-IIs.


 * In Halo: The Flood, the D77-TC Pelican's operational capacity is said to support a pilot, a copilot, a crew chief, and twelve passengers in the troop bay. According to the Halo: Combat Evolved strategy guide, the Pelican can operate with three crew members, ten seated passengers, and five standing passengers. In Halo: The Flood, Pelican Charlie 217 carries thirty Sangheili in the troop bay in addition to the human pilot and another Sangheili in the cockpit. In Halo: First Strike, Pelican Bravo 001 carries twenty-two Spartans, though the Spartans had removed all unnecessary equipment from the troop bay, including the seats, and were packed nearly shoulder-to-shoulder in the troop bay; Halo: Fall of Reach - Invasion, which rather loosely adapts the story of Red Team's insertion from First Strike, shows that the Pelican had an expanded bay and far more massive overall than normal Pelicans. Pelicans seen in-game feature ten seats and could easily accommodate around ten more standing passengers.


 * According to Halo: The Fall of Reach and First Strike, the SPARTAN-IIs wore identical MJOLNIR armor which lacked any identifying features, making it nearly impossible for an outsider to tell them apart.; Dr. Catherine Halsey only recognized the Spartans based on the subtleties of their movement. However, in later visual media they are shown displaying their numeric tags on their armor and wearing specialized MJOLNIR variants. Five SPARTAN-IIs (Jerome, Douglas, Alice, Cal, and Kelly) even had pinup art painted on their Mark IV suits.
 * This is a twofold retcon with both artistic and canonical merit. Such distinction is all but necessary in a visual medium, as depicting the Spartans as identical to one another could confuse the audience. While the Spartans could distinguish one another by body language, having their tags displayed could benefit any non-Spartan personnel they served alongside. The reason behind the Spartans' use of armor variants is more obvious: forgoing their use would be out of character, particularly for specialists who could make use of MOS-intended models. Indeed, Halo: The Essential Visual Guide unambiguously states that some MJOLNIR variants saw particularly widespread use among the SPARTAN-IIs. From a production standpoint, this is because The Fall of Reach and First Strike were released before Halo 3 introduced the concept of purpose-built armor permutations.


 * In Eric Nylund's books Halsey is often said to wear glasses, habitually pushing them up her nose. In each of her visual appearances (with the exception of Homecoming) Halsey does not wear glasses, while the Kilo-Five Trilogy simply makes no mention of them.

Inconsistencies rectified in re-releases
This is a list of disparities that remain in older novel editions, but have been retconned in later releases. For a complete list of changes in the re-releases, see here.

Halo: The Fall of Reach

 * In Halo: The Fall of Reach, the dropship used to transport the 75 SPARTAN-II children to the Military Wilderness Training Preserve was originally identified as a Pelican, whose troop bay would ostensibly be too small for 75 people. However, this was rectified in the 2010 reissue, in which the dropship is changed into a larger Albatross.


 * On page 46 of the original edition, Kelly handed out parts of a map to the seventy-five SPARTAN-II trainees. Then on page 48, when John checked to make sure the children arrived at the lake, he counted only sixty-seven...which seemed to be all of them. In the re-release, "sixty-seven" is changed to seventy-four.


 * In Chapter 22, James-005's left arm is burnt off by an assault cannon. In the original edition, it is said a few pages later that he saluted with his left hand–while it was still missing. In the 2010 re-release, he salutes with his right hand.


 * Captain Keyes refers to Ensign Lovell as "Michael" instead of "William". This has been fixed in the 2010 edition.


 * In the original, a UNSC frigate was referred to as the Alliance, and then shortly thereafter as the Allegiance. In the 2010 edition, the ship is referred to as the Allegiance in both instances.


 * In the original edition, the ship was referred to as a cruiser and then later as a carrier. In the 2010 edition, the ship is referred to as a cruiser in both cases.


 * On page 19, Michael Stanforth was said to be a Vice Admiral, and on page 95, it said he was a Rear Admiral. In the 2010 edition, he is referred to as a Vice Admiral in both instances.


 * The Pillar of Autumn was said to be missing its port-side emergency thrusters, but later used them twice. In the 2010 edition, the mention of the thrusters being missing has been removed.


 * During the Master Chief's mission to Reach Station Gamma, a Jackal's blood is said to be blue, although it is clearly purple in the games. The same mistake is made with the Elites, saying that their blood is green, while it too is purple.


 * In the original edition, the first time John-117 encounters Sangheili warriors in the battlefield is on Gamma Station during the Fall of Reach. In addition, the UNSC is depicted as not having any first-hand intelligence on the species prior to the battle; Dr. Halsey only speculates their existence. This has been largely ignored in later material, and Sangheili have been depicted as being present in battles throughout the war numerous times. References to the Sangheili as being a never-before-seen species were altered in the 2010 re-edition.

Halo: The Flood

 * The cutscene in Halo: Combat Evolved at the end of the level The Pillar of Autumn clearly shows the Autumn being fired upon with plasma. However, in Halo: The Flood, the Prophet assigned to the fleet forbids the Covenant ships to fire, lest they strike the "sacred relic". However, this is remedied in the fleet broadcast log in the ancillary content of the reissue of Halo: The Flood, where it is revealed that the order was ignored by the fleet's Supreme Commander.


 * The original edition describes how a group of entrenched Marines could not be hit by Ghosts' plasma fire, as the vehicles' plasma cannons were fixed and the marines were on a hill. In the games, the Ghost's plasma cannons can easily increase or decrease their angle. In the 2010 edition, the line is made more vague, stating the "Covenant vehicles couldn't get a fix on the Marines' position".


 * The original edition of the book consistently mistakes the 8-gauge M90 Shotgun as 12-gauge. This is corrected in the 2010 edition.


 * In the original edition, Sergeant Parker is consistently referred to as a he, and then a she. He is consistently referred to with the male pronoun in the new version.


 * In Chapter 9, the Second Squad was implied to have been completely consumed by the Flood, specifically saying that their numbers dwindled until two PFCs remained, before the last of the Marines fell. A page later, however, it is stated that there was little for Foehammer could do "except pick up the Marines, and hope for the best." In the 2010 edition, the part about picking up the Marines has been removed.


 * In Chapter 10 of the original version, it says that three weapons would be unwieldy for the Chief, not to mention "damned heavy." It then says he chose a shotgun and sniper rifle. During the ensuing engagement, it is then stated the Chief "switched to the pistol", despite the fact it was established he was only carrying a shotgun and a sniper rifle at the time. In the 2010 edition, "pistol" is changed to "shotgun".


 * In the original edition, First Lieutenant Melissa McKay's mission clock, seen in chapter headings, is prefixed by an extra 1, creating an inconsistency with the Master Chief's mission clock. This has been fixed in the 2010 edition.

Halo: First Strike

 * Similar to the inconsistency of the Spartans' first encounter with Sangheili, in Halo: First Strike, the Spartans did not have any prior knowledge of the Jiralhanae until their encounter with them on the Unyielding Hierophant during Operation: FIRST STRIKE. This has also been contradicted in multiple later works which show Brutes as being well known to UNSC forces throughout the war. Like the Sangheili encounter inconsistency in The Fall of Reach, in the re-release of First Strike, references to the Jiralhanae have been altered so that the Spartans are now familiar with them.


 * The Longsword used by the Master Chief and the other survivors from Installation 04 to land in the Ascendant Justice was repeatedly referred to as a Pelican in the original edition. The ship is consistently referenced as a Longsword in the reprint.


 * Vinh is referred to as "SPARTAN 029" twice in the original edition, even though the tag 029 is assigned to Joshua throughout the rest of the book. In the 2010 edition, Vinh is correctly referenced as "SPARTAN 030" in both instances.