Continuity mistake: When Daryl is driving the hospital van, it shows that he is going to land upside down, on the vehicle's roof, when he drives off the parking garage. In the next scene, the vehicle lands on its wheels, as if it has done a complete front flip. (00:30:00)
Continuity mistake: Before the Roadhouse fire, Ash and Dean are talking on the phone. Ash looks at his watch, on his left hand, it says 8:10, and has a black dial/face. As Dean and Bobby go through the rubble, Dean identifies Ash by his watch. Still on his left hand, it is now upside down, evident by the crown of the watch (used to move the hands of the watch) which previously facing his hand, is now facing his elbow. Also, the dial/face of the watch is now silver instead of black. This is a different watch, and was inadvertently put on the burnt arm upside down.
Factual error: When Steve and Nancy are making out, the intro to "A Hazy Shade of Winter" by The Bangles plays. While the original version of the song was released by folk-pop duo Simon and Garfunkel was released in 1968, the version heard here was released in 1986, 3 years after the scene takes place. (00:52:30 - 00:55:40)
Visible crew/equipment: When Mulder and Scully enter the abandoned mine through a doorway, the viewer can see at right in the distance a number of people sitting on a wall, and one crouching in front of the wall with what looks like a dog. They are sitting still, but there is still movement there. (00:16:00)
Continuity mistake: Charlie, Olivia's former partner and friend in the FBI shows up in this episode during the interview with Mrs. Rusk, but Charlie was killed off by one of the shapeshifters in a previous episode, and the shapeshifter that killed Charlie was himself killed off by Olivia, who in other episodes reflected back on killing him. This episode was supposedly meant to be in season 1 as ep 21 or 22. Unknown why they didn't air it then, and decided to put it in the middle of season 2 (for no apparent reason).
Continuity mistake: Near the start, the camera pans out to see the dome now covered in a layer of black. Outside of the dome you can see nice green fields, a small forest area, little houses and everything looks rosy. However a few episodes back the military launched a MOAB (mother of all bombs) and and the surrounding area was wiped out completely. (00:05:50)