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. (01:07:00)
Continuity mistake: When Sister Aloysius is walking Mrs. Miller to work, the Sister's umbrella handle is hooked to the left, then hooked to the right in the next shot. (01:12:10)
Revealing mistake: When Strahm's phone says "no signal" there is actually a three bar signal. (00:06:35)