The Red and the Black (2) - S5-E14
Revealing mistake: It seems that in the first shot the doctor injects something into the vaccine vial rather than extracting from it since the syringe plunger is moving inwards instead of outwards. In the next shot one can see that the syringe is being filled with the vaccine, however the arrangement of doctor's fingers is suitable for injection, which strongly suggests that the scene is played backwards. (00:17:55)
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