Other mistake: Being chased by Tooms underneath the escalator, Mulder climbs out of the manhole in front of the escalator, and hits the switch to activate the escalator. Tooms is then being dragged away from the manhole, but the direction of movement of the escalator below the floor would actually have dragged him towards the manhole where Mulder and Scully are.
Continuity mistake: Just before Skinner shoots Alex Krycek in the head, Alex is lying weakly on the ground, having already been shot twice. However, as Skinner makes the kill shot, Alex is suddenly standing and falls to the ground upon impact of the bullet, with no time (or strength) for him to have risen. Also, the last shot of the dead Alex shows his face and his nostrils flare from breathing.
Plot hole: The subject of the stakeout - the religious man dressed as a female prostitute to 'put the other prostitutes at ease' before trying to 'save' them - is shown when Scully is on the phone telling Mulder about it; the man has a very masculine face, a hairy stomach and is in no way convincing. It's extremely unlikely that such an obvious cross-dressed male would fool such a large amount of people.
Continuity mistake: When Mulder sits at the computer terminal in the census records room, we see two empty boxes on the screen, one for an ID and one for a password. The shot cuts to Mulder, then back to the screen and shows him typing the password, while the ID has already been typed in; it is very long and there wasn't time in between shots or nearly enough clicks of keys for Mulder to have entered that ID.
Continuity mistake: After Rob returns to his apartment after throwing out the trash bag with the bloody shirt inside, his mouth starts bleeding and he goes to the bathroom. He removes his false teeth and a few of his real teeth start falling out; he has a small smear of blood on his bottom lip when the camera is looking at him but his mouth is clean when the shot changes to his reflection in the mirror, with no time in between for him to wipe it.
Continuity mistake: Izzy unwraps a peanut butter sandwich and sets it on a bare tree stump as bait for 'the Great Mutato', then he steps away with the others. When we see the Great Mutato hurriedly put it down, a paper bag is suddenly sitting on the stump beside the bitten sandwich.
Revealing mistake: The dead Mrs. Sim is supposed to be nude in the bathtub, but for a brief second, a glimpse of her head and shoulders reveals the very top of a flesh-coloured modesty wrap covering her breasts. This may not be visible in a non-widescreen format release.
Other mistake: On the information text at the beginning of the scene telling the viewers where the scene is taking place, it is written as the "First Sovereign Bank of Pennslyvania" in "Harrisburg, Pennslyvania", instead of Pennsylvania, misspelling the name of the state both times.
Continuity mistake: Pusher loads the revolver with one bullet, leaving five chambers empty. When Mulder picks it up and points it at Pusher, the bullet can be seen in the cylinder, just to the right of the gun barrel. Later, when Mulder begins to slowly pull the trigger for the third time (aiming at Scully), we see the cylinder turn to Mulder's left. Problem is, with the bullet situated as it was when Mulder picked it up, the bullet would have moved to the barrel and been fired the first time he pulled the trigger, killing Pusher. Instead, it fires on the third pull.