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.
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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.
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.
Plot hole: Agent Spender watches in horror as Alex Krycek stabs the neck of an alien directly in front of him and the usual bubbling green blood spills out. In every other instance of a human being in such close proximity to the green blood, the person has immediately taken a painful reaction to the substance, including severe damage to the eyes. Spender however is completely unaffected, as is Krycek, who was also close enough to feel the effects.