Revealing mistake: When Mulder and Scully are talking to Theresa at the diner she suddenly gets a nosebleed. If you look closely at her forehead/nose you can see the flesh coloured tube that pumps the blood. (00:33:20)
Deep Throat - S1-E2
Revealing mistake: During the hard braking due to avoiding the collision with the unknown agency cars, notice that there are stunt people sitting in the car instead of Mulder and Scully. (00:21:15)
Deep Throat - S1-E2
Revealing mistake: Mulder pulls away from the hotel after telling Scully he is going to shower and then they'll leave. The tire marks from previous takes are visible on the pavement.
Revealing mistake: After Scully handcuffs Tooms to the bathtub there is a close up of his face and you can see the edge of his contact lens. (00:39:07)
Revealing mistake: At The Beginning of the episode Darlene burns her hand trying to open the door, she then puts on an oven mitt and opens the door. If you look closely though she still uses her other naked hand as well as the covered hand to open the door and her naked hand is completely unhurt.
Revealing mistake: While the computer is being infected with the virus, Peterson turns away from the screen to face Scully. Two seconds later, after the shot of Scully, the same shot is shown again but in reverse so that Peterson turns back to the screen. It's more obvious if you look at the weird way his eyes blink in the reversed shot. (00:39:50 - 00:41:32)
Revealing mistake: In the shot where Mulder is jumping as to avoid being burnt by fire set by Cecil the caretaker, it is easy to see that it's a stuntman instead of Mulder. (00:38:35)
Revealing mistake: When Mulder is examining the residue on the mouth of the deceased man in The Beginning, the dead body's right eye twitches.
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