Continuity mistake: When Mulder gets out of the car, it's dark outside, but when the helicopter comes, it is still daylight. (00:25:00)
Revealing mistake: When Edward aims the rifle out of the window, you can see the cap is still on the scope. (00:40:22)
Revealing mistake: When the sheet is pulled back from Mrs. McRoberts' body at the morgue, her eyelids flutter significantly despite being dead. (00:18:30)
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