Continuity mistake: When Chuck Burks is analyzing the pottery, we can see that one of the pieces has a broken edge. Seconds later, the image shows the piece of pottery with the border preserved. (00:17:12 - 00:18:17)
Visible crew/equipment: In the scene where Scully is performing the autopsy on Micah Hoffman, you can see a shadow of someone moving across the wall behind her. (00:23:35)
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