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).
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Character mistake: Mulder asks Scully about "the fourth commandment about obeying the Sabbath, the part when God made heaven and Earth " However, Scully as a Catholic should know that this is the third commandment for Catholics. This is also an indirect indication that Mulder was raised in Jewish religion.
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.
Factual error: When Suzanne Modeski retreats to the restroom with a pair of pliers to pull out her tooth, she is only gone for approximately 15 seconds before the gunmen follow her. For a petite woman to rip out a strong, healthy molar from her own mouth (which also had metal prongs underneath in her gum) would not take so little time, no matter how determined she was. It's also highly unlikely that the lack of anaesthetic would have allowed her to do so without making pained noises.
Factual error: The first time we see Ed's tattoo, it is supposed to have been freshly done and he even removes the new bandage. However, there is no blood or excess ink on his arm, no redness around the lines, no swelling at all; no way at all that it could be a fresh tattoo.
Continuity mistake: When Scully is searching through the pictures to find Sarah Kavanaugh and Sullivan Biddle, she turns the photographs over and they have a label on them to say who they are. Yet when the shot changes angle to show the photos from the back, the labels have disappeared.
Deliberate mistake: When Mulder is about to go into the metal detector he puts his gun on the counter. He goes through the metal detector on his cell phone but his keys set it off, when he steps through again it doesn't go off. No cell phones can go through metal detectors without setting it off.
Factual error: When Scully is performing the autopsy on Leonard Betts' severed head, she states "As remains are incomplete, all observations refer to a decapitated head." This phrasing is redundant. The proper terminology would be "disembodied head." As a medical doctor, Scully should know this.
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