Factual error: The flag in Skinner's office is hung upside-down. (00:28:00)
Visible crew/equipment: When Mulder climbs up the tower of the submarine, his shadow is visible, projected on a studio wall. (00:32:40)
Factual error: In the opening sequence, we see a nuclear attack submarine beneath the ice in the Arctic Ocean. When the captain orders the ship to surface, one of the crewmen mutters, "Surface to what? We're under 32 feet of glacial ice!" Except that they're not under "glacial ice," they're under Arctic sea ice, which ranges from about 6 feet thick in the summer to about 15 feet thick in the winter.
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