Character mistake: When Kritschgau is testing Mulder's remote viewing capabilities, he tells Mulder that he is at about 5% accuracy. However, Mulder got at least two right and not enough time had passed for him to have had 40 opportunities, so his percentage of accuracy should be higher than five.
Continuity mistake: Clyde Bruckman commits suicide by placing a plastic bag over his head until he asphyxiates. However, when Mulder and Scully first discover him you can see in the shot just before Scully holds his hands that there is no plastic bag around his head (may only be visible in widescreen format).
Other mistake: Unlike Mr Chaco, who has the brace clamped around his neck, Scully is clamped around the top of her head, which is a quite irrational way of executing a person, because the clamp does not serve as a stabilizer. In fact, in this arrangement, Scully is not fixed to the stand at all.
Other mistake: When Doggett starts clawing at the freshly plastered wall, he does so at just below his eye-level and blood starts pouring from the hole he makes. The dead woman inside the wall was stabbed in the lower abdomen; there's no way that blood from the abdominal wound would've seeped through the wall at the level he was digging.
Plot hole: When Mulder and Scully are going to the town/city where the disappearances took place Scully says they should stop so she can walk the dog. Mulder says OK because he has to ask for directions yet the next scene we see is Mulder and Scully interviewing Dr. Faraday. How did they find him if they didn't know where they were?. And after that we see them at a store where they do ask for directions.
Factual error: At the beginning of the scene, XO Johanson is looking through the periscope. However, it is nonsense, because the submarine was in silent running, and the Japanese destroyer was circling it, so the sub must have cruised in deep submersion. The water depth there was approx. 270 meters, as the French salvage team claims at the beginning of the episode. There is rarely any significant light beyond 200 meters. Looking through the periscope in these conditions would be completely useless.
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).
Add timeSerious B
Plot hole: Mulder is pulled from the escape hole previously dug by the hybrid aliens to escape the train car. When they pull him out they show alien bodies remaining in the hole. Mulder never revisits the train car despite knowing there's a high probability of finding hard evidence, in this case some actual bodies. There's no way Mulder would just assume there's no evidence remaining there and not go have a look for himself. Same goes for Cancerman who thought he had destroyed the evidence.
Deliberate mistake: When the unconscious, naked Asian doctor is removed from the warming tub, his hands are clasped over his crotch to protect his modesty, despite the fact that he shouldn't be able to do that, since he isn't conscious and his previously frozen limbs are now pliable and relaxed due to the heat.
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.
Plot hole: On the phone, Scully asks for the report on her sister to be sent to the San Diego F.B.I field office (since she is visiting her brother and his wife and so is not in Washington), but the package is sent to her brother's home. Even if 'Danny,' whom she asks for the file, decided to be helpful and send it directly to her, her brother's address is not likely to be the one in her personal file, plus she didn't mention that that's where she'd be staying.