While this is a direct continuation of My Struggle II (2016), with no time having passed between the two episodes, compared to it the pencils on the "I Want to Believe" poster have slightly changed positions and there are no more holes from pencils previously thrown at it.
(Around 25 minutes) Reyes puts her gun to the top of Skinner's head but in the next shot it's below his ear.
During the car chase, the dashboard speedometers show kilometers per hour (Canadian) rather than miles per hour (U.S.).
In the opening, where the Marlboro man is narrating, it is suggested that the Moon landings were faked. However, the studio settings shows the camera filming the actual foot of Neil Armstrong touching the Moon dust. This would be impossible since the camera on the outside of the Moon lander was at a different angle and height, not providing the actual foot touching the dust for the first time.
The opening moments show a television camera supposedly filming the fake Moon landings. However, in order to provide realistic fakery of the Moon landings, these types of television cameras would not be a logical choice since their quality was much better than the cameras on the Moon lander.
In Scully's hospital room there are some very convenient scalpels for Mulder to use.
When Skinner is pointing to the monitor displaying the fMRI of Scully's brain, he is pointing to the pre-frontal cortex not the hypothalamus as the neurologist claims.