Other mistake: Mulder pulls in to park in front of a red car. The front plate on both Mulder's and the red car is the same: 5S2 706. (00:27:37)
Continuity mistake: In the scene at the start, when the police car passes the truck, clearly it is daylight, but right after the truck shuts down it is completely dark. (00:03:25)
Plot hole: After less than 1 minute of investigation Scully found out that the photograph was bogus. It tells a lot about the "very best" specialists, mentioned by the Deep Throat later on, who had prepared the photo. (00:19:10)
Continuity mistake: When Scully changes the refill of her ball-pen, in the right shot she keeps it under the desk while in the next left shot she holds it over the desk. (00:12:20)
Continuity mistake: When Mulder walks around Scully, he passes her by, however in the next shot he is again behind her. (00:16:10)
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