Due to the numerous safety features built into elevators, it is impossible for them to fall down an elevator shaft if the cables break.
Some valves turn right in order to open, when the standard is to turn left.
In the graphical update, the Glock pistol is changed to a Beretta. While the Glock can fire underwater, the Beretta can't, yet both are shown to do so.
The 'tranquilizer gun' only fires lethal rounds.
U.S. forces are shelling areas where their own soldiers are located.
In the graphics update, the sub-machine gun is turned into a carbine which should fire 5.56mm ammunition but in the game fires 9mm ammunition. While it is possible that the security force of a facility be equipped with such a weapon, it is doubtful that the military be equipped thus.
Near the silo containing the large creature there is an H.E.V. charging station and a medkit, both in the ceiling - not a very accessible location.
In the Lambda Complex, there is a guard who cannot have gotten where he is without encountering a soldier.