Plot hole: The worm is supposed to increase production of a violent hormone, making the host incredibly violent and unable to control it. Yet the infected member of the group manages to hide it perfectly between making their first kill and being discovered by the rest.

Continuity: When Mulder is examining the paper which says "We are not who we are", the writing changes position in between shots.

Continuity: At the beginning when a man says: "We're not who we are", he says it differently when Scully watches the tape.