Factual error: When Mulder is walking out of the cabin in Spender's uniform, the soldiers try to stop him. This is impossible since he is an officer (a lieutenant judging from the shoulder-straps) and they are privates, so they cannot give him orders. The only thing they can do in this situation is to salute him.
Factual error: This episode begins with Scully doing a voice-over about the incredible nature of our universe. The scene is very impressive visually, and would have been from the aspect of her oral presentation had it not been for a major error in the script. She says (more than once) that the universe is made up of matter and gas. This should have been "matter and energy". Gas is a form of matter.