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).Phaneron
Plot hole: At his arrival at the Arecibo observatory, Mulder crushes the padlock on the door leading to the control building, and then he finds the native man, Jorge, in the toilet, who hid himself in the building. There's no way Jorge could enter the building and also lock himself in there with the padlock. (00:17:45)Chop Luftmysza
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.
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. (00:08:30)
Plot hole: Scully's statement that she was 23 when she wrote her senior thesis in college throws off her timeline of college, med school, residency, FBI Academy, Quantico teaching assignment for two years, and X-Files assignment at 28. Her undergraduate degree in Physics should have been completed when she was 20 or 21 to allow at least 4 or 5 years for her medical training. (00:41:35)
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.Purple_Girl
Plot hole: It is virtually impossible that such a conspiracy-experienced, cautious, and wise person as the Second Elder would be so naive and careless to just let the "Dr. Openshaw" faceless alien to his house, knowing from the CSM that Dr. Openshaw had died that evening. (00:15:10)Chop Luftmysza
Plot hole: Agent Spender watches in horror as Alex Krycek stabs the neck of an alien directly in front of him and the usual bubbling green blood spills out. In every other instance of a human being in such close proximity to the green blood, the person has immediately taken a painful reaction to the substance, including severe damage to the eyes. Spender however is completely unaffected, as is Krycek, who was also close enough to feel the effects.Purple_Girl
Plot hole: Big Mike was attacked by the creature, because his bulb was broken just for a couple of seconds. It would mean that even if something like this happened to somebody else by accident, this person would also be killed by the creature. That would drastically increase the kill rate in the community. (00:16:15)Chop Luftmysza
Plot hole: When Arthur wakes up on the bus, he sees an alien reflection in the window beside Josh, but it's not possible that the reflection could be seen at all - especially from the angle that Arthur first sees it - considering how much of the pillow is covering both Josh's face and the window. The pillow extends past Josh's face so he could lean on it as cushioning against the window, but somehow Arthur sees a full facial reflection.Purple_Girl
Plot hole: Josh Exley's 'real' face shouldn't be visible as a reflection on the window. It's not an illusion that he creates to fool people, whereby his real self could theoretically be seen in a reflective surface, but a complete physical change, as we've seen in many episodes of the X-files regarding the shape-changing abilities of the aliens. What his face appears to be while altered is essentially what it is, and the reflection should show as much.Purple_Girl
Plot hole: After Exley has gotten up after being hit by the ball, Dales notices green alien blood inside the glove where the back of Exley's head was resting. However, Exley was hit in the face, not the back of the head; not only was there no bleeding face wound while he was on the ground, but the glove was clean when Exley first gets up.Purple_Girl
Plot hole: When Arthur looks closely at the green alien blood on the baseball glove, he has no reaction to it, despite the continuous pattern in the show about the blood being incredibly toxic to humans, even from a distance. It should have badly hurt his eyes at the least.Purple_Girl
Visible crew/equipment: I don't know if this is visible in all formats, but on the newest UK release on DVD, watching in widescreen, it's amazingly obvious. When Mulder recovers from the vampire attack, he gets up from the floor and breaks up a chair to make a stake. There is a shot of his feet as he smashes the legs off and bends to pick up a piece. In the bottom left hand corner of the screen, you can see a crew member's hand carefully and quickly placing a piece of wood on top of the pile for Mulder to pick up.