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.
Plot hole: Mulder is pulled from the escape hole previously dug by the hybrid aliens to escape the train car. When they pull him out they show alien bodies remaining in the hole. Mulder never revisits the train car despite knowing there's a high probability of finding hard evidence, in this case some actual bodies. There's no way Mulder would just assume there's no evidence remaining there and not go have a look for himself. Same goes for Cancerman who thought he had destroyed the evidence.
Factual error: Mulder tells Scully that he is trying 27828 and it is not working. It is not surprising that it is not working, because the Napier constant is not 27828, it is 271828. Plus they somehow they know how many digits from this constant should be entered on the keyboards.
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.
Continuity mistake: In the mine with the medical records we see Samantha's file. In the season 1 episode "Conduit" we see the X-File Mulder opened on her. In the previous episode she is listed as Samantha T. Mulder and her birth date is 1/22/64. Here we see her name as Samantha Ann Mulder and her birth date as 11/21/65.
Continuity mistake: Clyde Bruckman commits suicide by placing a plastic bag over his head until he asphyxiates. However, when Mulder and Scully first discover him you can see in the shot just before Scully holds his hands that there is no plastic bag around his head (may only be visible in widescreen format).
Continuity mistake: Later in the episode a man bangs on an air conditioner to try and stop it from making noise. In the first scene you can tell air is moving because the streamers are moving. After he bangs on the unit the streamers stop moving. The air conditioner is still on.