When Mulder is in the library there is a stain on the right sleeve of his shirt, slightly below the shoulder. When Patterson enters the library, and wakes Mulder, the stain on his shirt has vanished.
When Mostow's cell shutter is opened, the light from the corridor is extremely bright, yet when Mulder and Scully enter the cell the light is less harsh. At the bottom right of the door as it is opened a crew member's leg can briefly be seen, presumably taking the first, brighter light out of the frame.
Toward the end of the episode Scully is in her apartment and hears a voice message left by Agent Nemhauser on her answering machine. She calls Nemhauser's cell # and Mulder, in Mostow's studio, answers it, having found the ringing phone where Nemhauser (now dead) left it. After a brief conversation Scully tells Mulder to stay there and that she will be there in a few minutes. She does indeed show up just several minutes later, in time to see Mulder pointing his gun at Agent Patterson. However the series had already established that Scully's home address is in Annapolis, Md., a good 30+ miles away from Washington DC where Mostow's studio is located. It would therefore be impossible for Scully to have arrived on the scene that quickly coming from her apartment.