During a car park fight scene between Mulder and X, X's stunt double is apparent on several occasions.
In the opening, the menu behind the burger bar has 6 images. 5 of these are of the same burger.
When Mulder's mother has a stroke due to arguing with "The Cigarette Man", she is taken to a nearby hospital, at 10:00, when Mulder enters his mother's hospital room, you can see the breathing tube in her mouth, then at 10:10, it's placed out of her mouth, this keep continuing throughout that scene.
The Virginian license plate on the Arlington County police car is an outdated one from the 1970s and was used on state-owned vehicles rather than county-owned ones.
When Scully is looking through the Social Security records for Jeremiah Smith, the Cupertino entry shows the zip code 95041. The correct zip code for Cupertino is 95014.