At 39 min. 55 sec. in when Scully is faced with a Tank in the games 2nd Level, the door to exit the game behind her is clearly open when moments before it's closed and Mulder is shown trying to pry it open with his sword.
When Mulder disappears into the game and Scully runs into the room at the top of the stairs, she is heard saying "Where's Mulder?" but her lips do not match what she is saying.