The Guard that Joanna knocks out at the start of the second mission land on his chest with his head facing away from the elevator door, but when he wakes up at the start of the third mission, his body is now facing the opposite direction, even though during this whole time he's supposed to be unconscious.
When the player uses the rocket launcher and a guard has no gun, he will move down to the floor and the fire bolt is visible on the guards hands. If you fire the rocket launcher at the guard holding the bolt, the game freezes and has to be reset.
In the first Area 51 level at the beginning when Daniel tells Joanna to attach a bug onto the antenna, the guards in that area have the dragon gun but during playing the level, they all have MagSec 4 guns.
In the 2nd Area 51 level when Joanna goes in to tell the doctors to step away from the alien, she is in lab clothes but in the cinema version of the clip, she's in her normal outfit.
On mission 1.3 when Dark is about to leave, the guards that stop her reload their pump shotguns by loading it as if it was a bolt action rifle.
Weapons eject to the left even though they would interfere with the wielder's movement. Most weapons are designed to eject from the right.
The receptionist with the brown dress appears in many levels, though it is not clear on what side she is on. as she seems to be working with DataDyne, and then with Joanna on a rescue mission at the Carrington Villa as an objective *Save the negotiator*.
In the mission 'Mr. Blonde's Revenge', several guards can be heard saying "Get her!". The problem is, in this mission the player plays a man.
In the Air Force One level, if the player places a timed mine on a guard's back legs, the guard is flown up through the ceiling into another room in the level once the timed mine is blown up after 5 seconds. Use the X-ray scanner to see the guard.
In the Nintendo 64 version when you shoot a guard or civilian with fire guns such as rocket launcher, devastator, etc., his/her face and clothes are burnt but in the Xbox 360 remake, this glitch is completely cut.
When you view the completed 2nd Area 51 mission, Joanna is stopping 2 guards from the alien sleeping. She is wearing lab clothes in the completed level but in the cinema version, she's in her normal clothes.