At one point during the game's development, lead level designer John Mulkey said to a fellow employee that he had seen a shadow in the restroom mirror. The employee agreed that the atmosphere in the room was "creepy", as there was a non-working light and one flickering one. John Mulkey insists that he saw something and, although no one seems to believe him, the restroom is hardly used anymore.
In the game there are several references to the sci-fi/horror movie Punto di non ritorno (1997). You can see a magazine cover in some levels that reads "Event Horizon found!". Also, on the multiplayer level "Asylum", there is a line written on the wall of a room that says "Liberate tu temet Ex Inferis", the same word heard in the distress call sent by the Event Horizon in the movie.
The name of the main antagonist, Alma, roughly translates from Latin to "nourishing one" and is the root for the phrase "Alma Mater" which literally translates to "fostering mother".
Jin Sun-Kwon was originally a sniper, although as work on the game progressed Monolith (the game designers) discovered that there were no scenarios where this could be implemented. Jin still has elbow guards and red index fingers on her gloves, i.e, her "trigger" fingers.
In the build shown during the director's commentary video, Paxton Fettel mentions Marshall Disler being the murder victim at the beginning crime scene of the game instead of Charles Habegger in the final game.