(at around 11 mins) When Mulder, Scully, and the sheriff are speaking outside the apartment building, the cut from the wide shot to the single of Mulder reveals the same wall in the background, but with different physical locations for the actors. In the wide, Mulder plants himself with the wall (reading "Manager's Office") directly to his right. In his close-up, the same wall is now behind him. This is either a blocking error for Duchovny or a very narrow area the camera could focus and the error is thus revealed through editing.
At 25 minutes, the motel room lampshades still have the plastic cover on from when they were brand new.
When Mulder, Scully and the sheriff are at the Church of the Red Museum, the woman reading what the leader is typing is saying the words before they appear on the screen. This happens several times during the scene.
When Scully is looking at the pictures of the family on the wall, a camera is visible in the reflection of the glass.
In the opening scene where Mulder and Scully are riding with the sheriff in Wisconsin, we see a white-capped mountain in the background. There are no mountains in Wisconsin.
One scene on main street in the Wisconsin town shows a business, TDH Fluid Systems. This is an Alberta, Canada, based industrial pump business with offices in British Columbia, but not the U.S.
Scully finds the chemical contains the same DNA they found in The Erlenmeyer Flask (1994), in the bovine hormone and says that it has unidentified amino acids. DNA does not contain amino acids; it contains nucleic acids.