Near the end of the movie, Scully's white Ford Taurus is parked outside, even though it had been wrecked earlier in the film. When Scully comes out of the house, a silver Ford Fusion is parked outside.
When Mulder finds the snowplow truck on the side of the road, and looks inside for the tire iron, the snowplow's roof lights are on. When Mulder walks away from the snowplow in the next shot, the roof lights are off.
When Scully is talking to Father Joe in the hospital after his cancer diagnosis, a shot from behind the Father's shoulder shows his head raised off the pillow. When the shot changes, his head is lying flat on his pillow.
Scully and Mulder fly in on a helicopter from their house. The rotor is still turning after they land and exit the helicopter, but Scully's and Mulder's hair remain in place. In the next shot, they walking away from the helicopter with the rotor still turning. The rotor wash would blow their hair around.
The first time Scully and Mulder accompany Father Joe to the scene of the agent's abduction, the sun is rising and the screen reads "Somerset, West Virginia, 5:02 AM". During mid-winter in that part of the country, it would still be completely dark at that hour.
When Mulder is following the pick up truck to the hide out he scrolls through his phone contacts and highlights what some viewers have claimed is the name 'Gillian', the first name of the actress who plays the character, Dana Scully. However, it actually says 'Gilligan'.