Plot hole: The ability of the Faceless Rebels to impersonate other people completely defies logic. For one, when impersonating someone, the Faceless Rebel is able to speak despite the fact that they mutilate their own mouths shut. Secondly, as can be seen in many instances when a person is being attacked by a Faceless Rebel, the face of the person they are impersonating is merely a skin mask that can easily be pulled off. If the face of the person they are impersonating is just a mask, then any time a Faceless Rebel speaks you should be able to see their true face through the open mouth of the skin mask. Additionally, the face of the person being impersonated being a mask would also preclude the Faceless Rebel from blinking or moving the mask's eyes (similarly they mutilate their own eyes shut, so the eyes of the skin mask can't be their own).
Continuity mistake: When Scully walks into Mulder's office, she stops in the position with the "I want to believe" poster in the background, then she takes a couple of steps to make acquaintance with Mulder, and she finds herself again in the position with the poster in the background. (00:05:15)
Continuity mistake: When Mulder and Scully are driving after their plane lands, we see at one point that Mulder has his left hand on the wheel and he is eating a sunflower seed with his right, yet when the shot changes he's driving with his right hand and eating with his left. (00:09:45)
Continuity mistake: When Scully is in her room after the autopsy, we see the x-ray attached to her lamp. When we first see it, we can see the letters LD on it, yet when the shot changes back to the x-ray after Mulder has gone, we can only see I, presumably the other x-ray is now overlapping it. (00:15:20 - 00:16:10)