Visible crew/equipment: Mulder talks to the man from NICAP on the other side of the fence. When the shot is looking at the man, film lights are visible reflected in his glasses. Since he is looking at Mulder, there should be lights on Mulder's side, but there are none.
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.
Add timeCharles Austin Miller
Other mistake: In order to leave such bloody footprints, CSM must have stepped into the puddle of blood. It is impossible because the guy shot by CSM could not bleed so much blood in such short time, not mentioning that CSM must have intentionally stepped into it.
Continuity mistake: While Mulder's waiting for Langly and Frohike to unlock the exit door, Gray-Haired Man keeps shooting at the glass door, and the increasing bullet damage on the glass doesn't stay consistent as more damage occurs, and changes between the closeups and wideshots.
Add timeSuper Grover
Continuity mistake: When Mulder is talking to Dana's mom about finding her cross (necklace) in the trunk, Scully's mom says that she gave it to her on her 15th birthday, but in Season 5 in Christmas Carol, Scully has a flashback to receiving it at Christmas.