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.
Continuity mistake: When Tooms is in the cell right at the end, we see when his food is being brought over to him on the tray that there is a drink and a bun, when the shot changes to the other side of the door the drink and bun have swapped sides. When the shot changes back to the other side of the door, the tray is now the other way around and then when the shot goes back to the other side the whole tray has now disappeared.
Audio problem: When Jerry uses the elevator, the voice of the computer reads out the floors as "twenty-third floor, fourth floor, fifth floor" etc, missing out the "twenty-" prefix until the 29th floor. The DVD subtitles list these numbers with their prefix, so this was not intentional.
Continuity mistake: When Scully is in her room after the autopsy, we see the x-ray attached to her lamp. When we first see it, we can see the letters LD on it, yet when the shot changes back to the x-ray after Mulder has gone, we can only see I, presumably the other x-ray is now overlapping it.
Continuity mistake: When Mulder and Scully are driving after their plane lands, we see at one point that Mulder has his left hand on the wheel and he is eating a sunflower seed with his right, yet when the shot changes he's driving with his right hand and eating with his left.