Continuity mistake: At the end of this episode when Mulder is talking to Marty through her jail cell, the position of their hands change. In one shot, Mulder's hand is covering hers, and in the next, each of their hands are gripping the cell bars. This goes back and forth a few times.
Continuity mistake: The dates on the academic discipline and progress forms for Max are not in accord with the order of the episode, coming after the "Millennium" episode. Supposedly the changes in his behavior and grades started a few months before, but the reports are from a few years ago.
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").
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.
Continuity mistake: At Mulder's 'funeral' around when there is a knock at the door, we see Frohike raise his bottle to take a swig. The shot cuts to facing Scully and we can see Frohike further in the background and his bottle is nowhere to be seen, when he should've been mid-swig.