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.
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)
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)
Plot hole: The very ending scene where Peter (in this version died in the ice as a boy so Walter's wife never met him) takes off some of the dust covers then picks up a toy airplane. The toy airplane he got as a child from ... Walter's wife when she was trying to placate him in an earlier episode for trying to run "home". This toy airplane wouldn't have been his as a child in this version of the universe. (00:42:00)
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)
Audio problem: 1897: Quentin challenges Barnabas by pulling a decorative sword from a wall display and pointing it at his throat. Unfortunately, the display wasn't all that well attached to the set wall. Though the camera pans away, you can hear a loud clunk as the piece falls, followed by the loud crash of shattering glass as it strikes and breaks a table lamp. You can also see the actors struggling very hard to keep straight faces as they continue with their lines.