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.
Continuity mistake: When they find the felled ancient tree, the stump that Mulder clambers up onto to investigate the growth rings has a distinctive crack at the center and the growth rings are irregular in shape. However the stump that we get a close up of has no crack and regular circular rings.
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.