The distance between the Pillar of Autumn's engine room and the checkpoints that the Player must travel to is much greater than the length of the ship itself.
Captain Keyes appears to be wearing the rank insignia of a Navy Lieutenant (two silver bars). While the officer in charge of any Naval ship is the "Captain," it seems unlikely that someone with Keyes' age and experience would only have progressed to Lieutenant. A Navy officer who holds the rank of Captain would wear a silver eagle, not two silver bars. It seems that the developer confused the rank insignia of a Captain in the Army, Air Force, and Marine Corps with that of a Captain in the Navy. It is possible that rank insignia are different in the future.
In the game, the UNSC are heavily based off the US military. So assuming this is true, Echo 419 is the incorrect way of identification for herself. She says "Pelican Echo Four-Nineteen" when she should be saying Papa Echo Four One Niner. Same applies to the other Pelicans. It is possible that identification terminology has changed in the future.
The barrel on the shotgun is much smaller than the 8 gauges that the series canon says that it is.
Captain Keyes hands the Master Chief an empty pistol. All firearms aboard a ship are kept loaded during action stations.
Cortana states that she called in a dropship that had heavy weapons aboard. She never is heard to have called the dropship.
The assault rifle's magazine holds 60 rounds of ammunition, which is much more than could possibly fit in it in the caliber that the assault rifle uses.
Cortana's chip is inserted into one terminal in the Halo and extracted from another. There is no explanation as to how it switched places.
The distance between the Pillar of Autumn's final checkpoints has slopes and curves that no spaceship designer would put in a ship.
On several occasions, Captain Keyes refers to individual Marines as "Soldier." Navy personnel do not address each other or Marines as "Soldier." While anyone serving in the armed forces could be considered to be a soldier, only Army personnel would be addressed in this manner.
Cortina varyingly refers to the Covenant as singular or in plural.