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").
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.
Continuity mistake: When Senator Richard Matheson tells Mulder about the four Japanese Nationals had been murdered, he says that the murders had occurred several weeks ago. But when Mulder brings Scully up to speed a scene or two later, he tells her that someone must have been able to identify the four doctors who were performing the autopsy because they were murdered YESTERDAY.