Dæmonicus - S9-E3
Revealing mistake: At the very beginning of the episode, we see the reflection of the Moon in a puddle. The Moon looks exactly as we see it in the sky. The problem is that in the puddle we should see the mirror image of the Moon. (00:00:05)
Trust No 1 - S9-E6
Revealing mistake: When Agent Reyes drives up to Agent Dogget's parked car, he looks in his rearview mirror. Its background should be obviously a transparent windshield to which the mirror is fixed. However, when the camera shows the image seen in the rearview mirror, we see in the background something similar in appearance to a solid wall. (00:10:50)
Improbable - S9-E13
Revealing mistake: When Scully is examining the body of Vicky Louise Burdick, the dead woman moves her eyeballs. (00:22:50)
Trust No 1 - S9-E6
Revealing mistake: When Doggett visits Scully in Quantico and interrupts her pathology class, the cadaver left on the table blinks his eyes at least twice. (00:28:25)
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