Other mistake: An agent and Scully analyze the fragment taken out from Duane Berry's body. The agent draws Scully's attention to "small markings", which are half a monitor size, and Scully naively asks where they are. (00:39:00)
One Breath - S2-E8
Other mistake: At The Beginning of the episode, a gravestone for Scully is shown. However, it seems as if less than a week passes between Scully's mother and sister deciding to let her go and Scully waking up. It's unlikely that the gravestone business would have the stone ready in such a short time.
Other mistake: Unlike Mr Chaco, who has the brace clamped around his neck, Scully is clamped around the top of her head, which is a quite irrational way of executing a person, because the clamp does not serve as a stabilizer. In fact, in this arrangement, Scully is not fixed to the stand at all. (00:38:15)
Anasazi (1) - S2-E25
Other mistake: Immediately after a shot has been heard, Mulder, who is in flat #42, grabs his gun and rushes through the corridor passing by flat #47, which means he is still on the same floor. Within 10 seconds after the shot, the next-door lady is already aware of the crime. Not mentioning that 2 seconds later two policemen arrive at the scene. (00:07:21)
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