Visible crew/equipment: When Mulder and Scully enter the abandoned mine through a doorway, the viewer can see at right in the distance a number of people sitting on a wall, and one crouching in front of the wall with what looks like a dog. They are sitting still, but there is still movement there. (00:16:00)
Continuity mistake: When Mulder experiences his near-death trance state his body is lying, apparently lifeless, in a star spangled sky. As the camera tracks in on him the toes on his right foot twitch, just after Deep Throat begins to speak. The foliage covering his chest also changes position between shots. In the wide shot he is covered up to the armpits. But the first close up shows his chest is exposed. Then in later close ups it is covered again. (00:14:25)
Continuity mistake: When Skinner walks into the cafe (the time he gets shot) another man is just walking out, leaving a table with a used glass and coffee cup. The waitress is in the back, getting Skinner a cup of coffee (she couldn't have cleaned the other table yet), but when we look over Skinner's shoulder you can see that the other table is cleared and has a clean coffee cup (turned upside down) on it.
Factual error: In the scene where Mulder, the police officer and the doctor are in the doctor's room, the time on the clock reads 8:40. The doctor announces that he going to the bathroom. The scene cuts to him in the bathroom and then back to the doctor's office with Mulder and the police officer. Another cop comes in and says, "Come to the bathroom, something's happened." The clock still reads 8:40.
Factual error: After the agents meet with Kevin's father in the mental institute, Scully lists the medication that he is on: haloperidol, loxapine, and chlorpromazine make sense, but the fourth medication - LARGACTIL - is in error. Not only is it a brand-name of chlorpromazine, but it is not available in the USA, it is a CANADIAN drug. (00:36:10)
Continuity mistake: When Scully and Mulder first visit John Mostow he says that he drew all the pictures of Gargoyles, which would have been a pretty good act considering he was in a strait jacket and would not have been allowed to have paper and drawing materials anyway. (00:07:30)
Continuity mistake: When Senator Richard Matheson tells Mulder about the four Japanese Nationals had been murdered, he says that the murders had occurred several weeks ago. But when Mulder brings Scully up to speed a scene or two later, he tells her that someone must have been able to identify the four doctors who were performing the autopsy because they were murdered YESTERDAY. (00:30:05 - 00:33:10)