You start the Facility stage by recreating the scene from the movie dropping in on a guard in a toilet stall doing his business. However, in the game, the guards in the bathroom stalls are standing at attention, fully clothed, facing away from the toilet.
On the second trip to the Severnaya Bunker, the player is tasked with retrieving CCTV footage showing their capture at the end of the previous mission. What does the VHS tape containing the footage look like in-game and in the player's inventory? A copy of the movie!
Any time you're in an elevator, the music is overriden with elevator music.
Turning on the floating mine cheat can lead to some of the best fun in the whole game. Walking around leaving a hovering trail of remote mines behind you just to watch the pretty explosions afterwards can make it all worthwhile.