The amount of blood on Mulder's lip changes frequently.
When Scully walks into AD Skinner's office to discuss the autopsy she is to perform, there is visibly no magazine loaded into Skinner's gun when he stands up and walks towards the camera.
When Mulder is talking to Scully after the hostage situation, he incorrectly refers to Helsinki Syndrome. The correct clinical name is Stockholm syndrome. (Though it is possible that this is a jokey reference to the same error in Die Hard (1988).)
When Scully is examining the shooting victim's body for the second time and looking at the back of his neck for bite marks, she shaves a small area and then blows away the hairs. By blowing on the body, she was contaminating it with her own DNA, thus negating any chance of getting a clean sample of DNA or trace evidence from the perpetrator.