Audio problem: The first scene following the intro, when Mulder and Scully step out of the car, Scully says, "I still don't get it" but her mouth doesn't move. (00:02:30)

Continuity mistake: In the close-up shot of Mulder just before he shoots Barnett, his black ear piece disappears. (00:42:15)
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