Factual error: When Mulder is walking out of the cabin in Spender's uniform, the soldiers try to stop him. This is impossible since he is an officer (a lieutenant judging from the shoulder-straps) and they are privates, so they cannot give him orders. The only thing they can do in this situation is to salute him.
Visible crew/equipment: When Mulder is driving away from the gas station, crew members as well as some filming equipment can be seen reflected in the car's body. Mulder is in a pretty desolate area, so seeing people reflected in the car's body would in all likelihood be crew members and not random citizens.
Revealing mistake: When Mulder - whilst trapped in the body of Morris Fletcher - is doing various poses in front of the mirror, several of his movements and the corresponding movements from the realized reflection of Morris Fletcher are slightly out of sync with each other.
Add timeSerious B
Continuity mistake: During the conversation with Scully regarding Wayne Weinsider, Mulder says "I don't know why. I'm not a psychologist", which must be a big surprise for all viewers, to say the least. Mulder graduated from Oxford University with a Bachelor of Arts degree in Psychology (e.g. "Dreamland II") and he worked for some time as a profiler for the FBI (e.g. "Young at Heart").
Continuity mistake: Malcolm Wiggins stabs Alfred Fellig in the back three times, including once in the middle of his back to the right of his spine. However, when Scully is examining Fellig's back later in the episode, he has at least six stab wounds, and all of them are around his shoulder blades.
New this week Continuity mistake: When doctors make a cut on Cassandra's belly, the green substance comes out of the cut and pours down directly onto the piece of blue cloth she is covered with. In the next shot the fragment of cloth that was in contact with the substance is dry, but in the following shot, there is a large soaked stain on the piece of cloth.
Plot hole: It is virtually impossible that such a conspiracy-experienced, cautious, and wise person as the Second Elder would be so naive and careless to just let the "Dr. Openshaw" faceless alien to his house, knowing from the CSM that Dr. Openshaw had died that evening.