Throughout the game, none of the characters are able to see Paxton (aside from Point Man, Alma, and the Creep) However, when actually playing, all of the characters are able to see him.
While Paxton Fettel is shown constantly walking through walls in his ghost state, the players are unable to do the same even when Paxton has not possessed anyone.
Despite being imprisoned by Armacham soldiers for nine months since his capture in the last game, Sgt. Becket is shown to have the same hair cut and is still permitted to wear all of his tactical gear.
The MP-970 sub-machine gun appears to have no ejection port. Despite this, shells are still ejected.
Becket and the Point Man are both telepathic, yet they can't read each other's minds.
Measurements in the game are in metric. The U.S.A. uses Imperial measurements.
Becket is shown being able to kill people using their own guns against them, a dangerous force even when unarmed and even capable of telekinetic manipulation (given how he drove Alma away from him at the end of F.E.A.R. 2). Despite these strengths, he is somehow unable to escape nine months of confinement, something he would have done given his aggression and hatred toward Alma and the ATC.