Continuity mistake: When Mulder cuts out the article about "Dr. Frankenstein", the cut is just above the article title, but when he tacks up the article it includes the heading of the 'Times Dispatch'. Then in its close-up the paper is cut just above the article title again and it continues to go back and forth in following shots.
Continuity mistake: When Dacyshyn drags Mulder by his legs and brings him to the shed, he goes past the tree stump with an axe embedded in it, but in the close-up of Mulder's torso there is some debris on the tree stump and the axe has disappeared, then the axe reappears still embedded in the wood.
Continuity mistake: When the FBI are searching the office, Dacyshyn walks out, sees Mulder, drops the donor bag and runs with Mulder and Agent Whitney in pursuit. The donor bag is rear-facing when he drops it, but in the close-up it's front-facing to show the words "human organ for transplant", and its straps positions also change between all shots.
Continuity mistake: When Mulder is hit by the truck from the Russian guy and his car tumbles off the road, you first see the driver seat window getting broken by the impact. Just before the car tumbles off the road and you see Mulder inside the car, the driver seat window reappears and does not seem to be broken. If you look carefully, you can see that the window is closed.