Visible crew/equipment: As the camera flies over the train, in the upper right corner of the screen there is some equipment and umbrella visible that are not likely to just be in the middle of nowhere - probably filming equipment. In the next shot they are gone. (00:31:05)
Visible crew/equipment: When Mulder climbs up the tower of the submarine, his shadow is visible, projected on a studio wall. (00:32:40)
Revelations - S3-E11
Visible crew/equipment: The camera and its operator are visible in a piece of metal on the back of the ambulance, when the mother is taken away after the accident.
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