Continuity mistake: After the part where the head Kindred woman tells Mulder and Scully "I asked you not to interfere", Mulder leads Scully away. From one camera angle, he is leading her away by the hand. In the same scene, but from a different camera angle, he has his arm around her. When we go back to the first camera angle, he is once again leading her away by the hand.
Factual error: After the agents meet with Kevin's father in the mental institute, Scully lists the medication that he is on: haloperidol, loxapine, and chlorpromazine make sense, but the fourth medication - LARGACTIL - is in error. Not only is it a brand-name of chlorpromazine, but it is not available in the USA, it is a CANADIAN drug.
Continuity mistake: In this episode, both Mulder and Scully say that the last time they were in Oregon was 7 years ago. A previous episode this season dealt with the millennium, so we know this episode took place in 2000. So seven years ago would be 1993, the year the show first aired. But in the Pilot episode, the corner of the screen reads their location in Oregon and March 7, 1992. 8 years ago.
Factual error: When Scully is performing the autopsy on Leonard Betts' severed head, she states "As remains are incomplete, all observations refer to a decapitated head." This phrasing is redundant. The proper terminology would be "disembodied head." As a medical doctor, Scully should know this.
Deliberate mistake: When Mulder is about to go into the metal detector he puts his gun on the counter. He goes through the metal detector on his cell phone but his keys set it off, when he steps through again it doesn't go off. No cell phones can go through metal detectors without setting it off.
Audio problem: When Jerry uses the elevator, the voice of the computer reads out the floors as "twenty-third floor, fourth floor, fifth floor" etc, missing out the "twenty-" prefix until the 29th floor. The DVD subtitles list these numbers with their prefix, so this was not intentional.
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.