The start of the game is said to overlap with the end of the original. However, the depiction of the time from Alma's release to the detonation of the Origin facility is substantially shorter than that of the original game.
The 'Armacham Assessment Briefing' booklet describes how Alma was not awake for the birth of the second prototype. This is contradicted by what Terry Halford states in the game about how Alma "woke up for that one too."
One of the files the player can discover in the game provides a detailed description of the sniper rifle. This file claims the rifle is semi-automatic, but the animation of the player-character clearly shows him manually cycling the bolt with each shot, making the sniper rifle a bolt-action rifle, not semi-automatic.
During the second Interval, the player witnesses an ATC soldier shooting a doctor. The player is actually left in control, can activate Slow-Mo and can feasibly shoot the ATC soldier and save the doctor. However, neither the soldier nor the doctor react to the activated Slow-Mo or player attacks. This also happens another time with the same result.
During the mission to converge on the nurse's office, the player encounters a Replica Forces helicopter rope-dropping soldiers onto the rooftop the player is advancing on. The player could feasibly shoot the chopper down having acquired a missile launcher from a previous mech fight. However, the chopper continues to hover in place even after the player has unloaded the missile launcher at it.
The rate of fire of the sub-machine gun is slower if wielded by enemy forces than if the Player wields it.
The mechanized suit uses metric measurements. Since the suit is presumably built in the U.S.A., it is more likely to be using Imperial measurements.
The grate the Player passes through to enter the school is not held up by anything when opened. Considering that it is a heavy metal grate, it should just slam closed if not held open.
Many of the Replica forces activated throughout the game lack psychic commanders to give their orders and Halford explains this is Alma's doing. This is contradicted by the fact that Alma is not a psychic commander, has never been known to use the Replicas and is even responsible for killing many of them.
The amount of fire-arms training that Delta Force operators receive borders on legendary, yet the player-character and his team members, all of whom are supposed to be members of Delta Force, commit basic firearms safety errors including: keeping their fingers on the triggers of their weapons without having a target in sight, casually pointing their weapons at each other while riding in the APC, and storing loaded weapons in the APC (these are visible behind the driver). Anyone who has completed Basic Combat Training, let alone Delta Force selection, would have enough knowledge of firearms not to commit these errors.
Genevive Aristide is depicted as staying very close to the same area that the first F.E.A.R. takes place in. Despite her desires to activate Project Harbinger, her staying anywhere near the settings of the first F.E.A.R. are illogical: she would have been apprehended much faster (and probably by a different Delta Force team), her previously confident phone calls to The Senator are contradicted from the first game and there's no reason why someone facing charges of crimes against humanity would want to stay close to the same Special Forces team she's corresponding with.