When talking to Scully in the hospital, Willmore says there has been more burn victims, when in fact there has been only one. He also says he has encountered the unidentified man twice, when at that stage of the game he has only been encountered once.
During a conversation with Mulder, the player is given the option of saying "Frohike sends his love." Frohike never says his name during his conversation with Willmore. Willmore even goes on to refer to Frohike and the other Gunmen as "three men via video conference."
A major plot point involves using the stiletto blade the kill the black oil entity by stabbing the host in the back of the neck. This is actually a continuity error as it is established in the television series that the stiletto blade is used to kill alien bounty hunters, not black oil hosts.
The only way to get Scully to trust you is to show her the alien blade given to you by X. At this stage of the series, which is disclosed as season 3, Scully has never seen the blade and even goes on to say that she doesn't know what the alien blade is in the same conversation.
In a "game over" scene wher Mulder is killed, Mulder is still blinking despite being dead.
Whilst describing her plan to lure Mulder into the isolation chamber and trap him there, Gillian Anderson noticeably flubs a few lines of dialogue.
In the game, the US Army has a denied operations base in Alaska, which is used for detaining and experimenting upon aliens, while using the presence of the Aurora Borealis to camouflage the flights of alien space vessels. The supposed longitude and latitude coordinates of the secret base are displayed on the screen on two occasions. The base is obviously located on land, since you can see the outside and can walk around the inside, and after all, the troops that attack you are not floating in water wearing diving equipment. However, it is interesting that in reality, the specified coordinates are underwater, off of Dall Island in Alaska. In a recent census, Dall Island had a population of twenty people.