Visible crew/equipment: After talking to the scientist about his car, Mulder and Scully are talking in front of a door. In the glass of the door is a reflection of a third person.
Other mistake: Deep Throat says that Mulder and Scully are standing in the very room, where "the first human-alien hybrid was created." However, only in the "Patient X" episode, are we told that it is Cassandra who has just become the first successful human-alien hybrid. (00:28:00)
Continuity mistake: When the Smoking Man brings the alien fetus to the Pentagon storage facility, he places it on the second rack, then in the next shot he walks away from the rack situated in the middle of the corridor. (00:42:55)
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