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). (00:42:55)
Continuity mistake: When Mulder is in the tram car ascending the mountain to rescue Scully, he pulls all of the things out of under the top left-hand seat, but when the scene moves to Krycek in the booth, you don't see any of the things that Mulder threw out. (00:19:40 - 00:20:50)
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. (00:39:40)
Continuity mistake: When Mulder and Scully are moving into the house, there is a shot of Mulder's watchface which reads that the date is the 7th. A few minutes later, Scully is walking around with a video camera, and narrating and she says the date is February the 24th. (00:08:35 - 00:09:30)
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.
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. (00:15:20 - 00:16:10)