Character mistake: When they exit the bowling alley with the dog, the dog is never put in the car, only the cage.
Character mistake: Mulder and Scully sneak into the morgue at Bethesda Naval Hospital to view the body of the dead fireman from the bomb blast. Mulder lifts the sheet back on the body to show that the man's tissue is "like jelly." Scully surmises there's been some kind of cellular breakdown, and then says the tissue is "completely edematous." However, Dr. Scully mispronounces "edematous" as ed-a-may-shuss. The correct pronunciation is i-dem-a-tuss. Being a doctor she'd know the difference. (00:37:45)
Character mistake: In the scene when Gillian and Sally are dragging the boyfriend in to put him on the table Gillian says, "Watch his balls Sal". It is in Nicole Kidman's native Australian accent and the rest of the movie she speaks with a Northeastern US accent.
Character mistake: When Marion is calculating how much she spent her math is wrong. The movie shows 400000 - 4036 = 395963. It should be 395964.
Character mistake: When Murdoch finds the correct page in the phonebook, it is not sorted correctly. e.g. "Harber G" should be before "Harber TJ" and "Harrison Dale" should be before "Harrison E" (00:44:18)