Revealing mistake: While the computer is being infected with the virus, Peterson turns away from the screen to face Scully. Two seconds later, after the shot of Scully, the same shot is shown again but in reverse so that Peterson turns back to the screen. It's more obvious if you look at the weird way his eyes blink in the reversed shot.
Continuity mistake: When Tooms is in the cell right at the end, we see when his food is being brought over to him on the tray that there is a drink and a bun, when the shot changes to the other side of the door the drink and bun have swapped sides. When the shot changes back to the other side of the door, the tray is now the other way around and then when the shot goes back to the other side the whole tray has now disappeared.
Audio problem: When Jerry uses the elevator, the voice of the computer reads out the floors as "twenty-third floor, fourth floor, fifth floor" etc, missing out the "twenty-" prefix until the 29th floor. The DVD subtitles list these numbers with their prefix, so this was not intentional.
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.
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.
Continuity mistake: When they find the felled ancient tree, the stump that Mulder clambers up onto to investigate the growth rings has a distinctive crack at the center and the growth rings are irregular in shape. However the stump that we get a close up of has no crack and regular circular rings.
Other mistake: In the scene where Mulder and Scully are first visiting Darlene Morris, there is a split-second shot of Mulder examining residue on his fingers that is edited in between Mulder and Scully ascending the steps to the porch and knocking on the door. It's as if the sequence was initially longer with Mulder discovering a suspicious substance before he and Scully knocked on the door that was not completely edited out.
Continuity mistake: After the part where the head Kindred woman tells Mulder and Scully "I asked you not to interfere", Mulder leads Scully away. From one camera angle, he is leading her away by the hand. In the same scene, but from a different camera angle, he has his arm around her. When we go back to the first camera angle, he is once again leading her away by the hand.
Continuity mistake: When Scully is reading report from Simmons' death, we can see that is has occured on the 7th of November, 1993; which means that whole episode takes place at the very beginning of November, but at the same time Scully and Mulder should be at Alaska (see episode "Ice").
Continuity mistake: When Mulder, Scully and the other police officers are digging Ray Soames's grave, one strap of the coffin breaks and the coffin falls and starts to roll. When it hits a tomb stone and opens, you can see there's a normal size body in the coffin. When they look into the coffin, there's this small alien body.
Factual error: At the crime scene where Roland killed one of the professors by dunking his head in liquid nitrogen and dropped him on the floor, someone has drawn an outline of the dead prof's body and all the bits his head broke into when Roland dropped him. This outline-drawing doesn't happen in life because it interferes with the crime scene, it's a popular myth.
Other mistake: Eve 6 says that ordinary human beings have 46 chromosomes, while the Adams and the Eves have 56 chromosomes. This makes 10 additional chromosomes. However, Eve 6 also mentions that they have additional chromosomes number 4, 5, 12, 16, and 22 - only 5 additional chromosomes.
Factual error: According to the NASA space shuttle launch countdown procedure, the close-out crew retreats to fallback area in the "T-3 hours and counting" phase. The members of the crew are the last persons who leave the launch pad at least 20 minutes before liftoff. However, during the close-up take of the main engines, when the ground control says "All systems go for APU start", we can see two members of the ground personnel in orange suits near the engines.
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.
Visible crew/equipment: Mulder talks to the man from NICAP on the other side of the fence. When the shot is looking at the man, film lights are visible reflected in his glasses. Since he is looking at Mulder, there should be lights on Mulder's side, but there are none.
Continuity mistake: Just as Mulder and Scully are entering the interrogation room to question Lauren for the second time, Mulder is holding a thin stack of paper, folded in half in his right hand. In one shot, these are folded horizontally. In the immediate next shot, they are now folded vertically.
Other mistake: Being chased by Tooms underneath the escalator, Mulder climbs out of the manhole in front of the escalator, and hits the switch to activate the escalator. Tooms is then being dragged away from the manhole, but the direction of movement of the escalator below the floor would actually have dragged him towards the manhole where Mulder and Scully are.