Continuity mistake: When Scully points out the location of the last time they saw Gibson Praise, she points to the (real) Palo Verde Nuclear Plant, which is west of Phoenix. In 'The Beginning' the plant shown was the (fictional) Rolling Hills Nuclear Plant, 60 miles east of Phoenix.
Continuity mistake: When the psychic collapses, sun is streaming through the window, indicating early afternoon. When we see the ambulance driving away a few scenes later, it's dark outside. It's highly unlikely it took a medic team several hours to get there and stabilise her.
Continuity mistake: When Scully finishes her conversation with Doggett and walks away, there is only one dark-haired policeman watching the crime scene, but when Doggett looks at the crime scene and Mr. Underwood gets up, there is a blond-haired policeman talking with someone.
Continuity mistake: When Doggett and Skinner visit Dr. Andre Bormanis at his place, in the first shot from the back he is leaning over some laboratory gear that is holding in his hands, while in the next front shot he is standing upright manipulating on the table with his hands.
Continuity mistake: When Knowle Rohrer is talking with Agent Doggett face to face in a separate room about the super-soldier project, he is wearing a red FBI badge, but in the previous scene when he came to visit Doggett, he was wearing a regular FBI badge.
Continuity mistake: When Agent Reyes is aiming at the oncoming car of a ranger, in the front shot the windscreen of the car is completely covered with dirt and fully opaque, while filmed from the ranger's side the windscreen seems to be transparent and relatively clean.
Continuity mistake: When Scully enters her apartment, the blinds are up and there is quite a lot of light in the room. However, when the flashback with Mulder ends, during which Scully was supposedly standing still, the shades are rolled down and there is much less light in the room.
Revealing mistake: The establishing shot of Boston General Hospital at the end of the episode shows the same building that was used for the BYU Medical Center in Provo, Utah eight episodes earlier in "Roadrunners" (note the vegetation under the part of the building that extends over the curb and the lettering on the building that says "Entry A"). The actual building is presumably in Kansas since the Kansas state flag was visible outside the building in the aforementioned episode.
Continuity mistake: In this episode the character of Billy Underwood was played by twin brothers Kyle and Ryan Pepi. If you pay attention you can tell when one twin was being used instead of the other as one of them has two freckles on his neck and another two by his right eye whereas the other does not.
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Continuity mistake: Just before Skinner shoots Alex Krycek in the head, Alex is lying weakly on the ground, having already been shot twice. However, as Skinner makes the kill shot, Alex is suddenly standing and falls to the ground upon impact of the bullet, with no time (or strength) for him to have risen. Also, the last shot of the dead Alex shows his face and his nostrils flare from breathing.
Continuity mistake: When Mulder sits at the computer terminal in the census records room, we see two empty boxes on the screen, one for an ID and one for a password. The shot cuts to Mulder, then back to the screen and shows him typing the password, while the ID has already been typed in; it is very long and there wasn't time in between shots or nearly enough clicks of keys for Mulder to have entered that ID.