Continuity mistake: When Mulder and Byers find Scully in Penny's room, there is a black stripe on the ceiling of the corridor, while in the scene when Scully is leaving the room there is no stripe there. (00:36:50)
Continuity mistake: While Mulder's waiting for Langly and Frohike to unlock the exit door, Gray-Haired Man keeps shooting at the glass door, and the increasing bullet damage on the glass doesn't stay consistent as more damage occurs, and changes between the closeups and wideshots.
Answer: As he stated many times throughout the series, Mulder needed Scully to be sober and skeptical. Whenever Scully's skepticism wavered and she started questioning her own rationality, Mulder would try to restore her sense of skepticism, because he needed her to be clear-thinking.
Charles Austin Miller