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. (00:37:30)
Factual error: Dogget says that "It would require something 4,300 times the density of steel to cause this damage." Steel is about 8 times denser than human flesh, so bearing in mind that density is proportional to mass at constant volume, it means that Ray would be 4,300 x 8 = 34,400 times heavier than if he were a regular human being. Assuming that he normally weighed about 80 kg, after the transformation he would weigh 80 kg x 34,400 = 2,752 tons. It means that hardly any ground would support his incredibly huge mass, let alone items such as a bed, chair, stairs, building structures, etc.
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. (00:41:55)
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. (00:18:10)
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. (00:08:40)
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. (00:17:00)
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. (00:20:30)