Factual error: The townspeople contracted Creutzfeldt-Jakob disease (CJD) from the bodies they consumed and it showed up in the brain tissue within a matter of weeks. However, this extremely rare disease takes several years to even be detectable. (00:18:55)
Anasazi (1) - S2-E25
Visible crew/equipment: As Scully stands up to leave at the offices of the Navajo Nation, the reflection of a boom mike moving in one of the picture frames on the wall can be seen. (00:19:40)
Factual error: Mulder says that the events occur near I-10, however, I-10 is nearly 200 miles south of Arkansas's border in southern Louisiana.
Factual error: Scully reads to Mulder from a book all about flukes (Trematodes). However, the information she is quoting is wrong. She states that flukes or flatworms have a "scolex" with hooks and suckers. These are actually the distinguishing characteristic of cestodes (tapeworms). Trematodes have no scolex and definitely no hooks. (00:17:30)
Anasazi (1) - S2-E25
Other mistake: Immediately after a shot has been heard, Mulder, who is in flat #42, grabs his gun and rushes through the corridor passing by flat #47, which means he is still on the same floor. Within 10 seconds after the shot, the next-door lady is already aware of the crime. Not mentioning that 2 seconds later two policemen arrive at the scene. (00:07:21)
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)
Visible crew/equipment: When the tiger is on the loose it prowls around a building site and there is a shot where you can see the animal trainer calling the tiger right to him. (00:23:56)
Visible crew/equipment: As Scully rolls down the stairs with the killer at The End of the episode, once they reach the bottom a hand pops out from the left side of the screen.
Continuity mistake: When Mulder gets out of the car, it's dark outside, but when the helicopter comes, it is still daylight. (00:25:00)
Continuity mistake: When Mulder pulls the nail from Blockhead's nose, the pliers are at The End of the nail, but in later shots it changes to the middle and then back to The End.
Soft Light - S2-E23
Plot hole: If the shadow acts like a black hole and tears apart all atoms that enter it why does it only seem to affect people (but also their clothing and anything else on them)? Surely Dr Banton would be destroying everything around him.
Anasazi (1) - S2-E25
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. (00:09:25)
Factual error: It's quite strange that only after Mulder looks into the ashtray he realizes that the Smoking Man has been in the car. Mulder should smell the scent of cigarettes immediately after entering the car, especially if he is a non-smoker. (00:36:05)
Revealing mistake: At The Beginning of the episode we see Duane being abducted and he begins to scream. Look at the "alien" on the left of the screen near to the top of the bed and you will see him move his head revealing where the suit ends and neck/head begins. (00:02:12)
Continuity mistake: Towards The End of the episode there is a scene where Mulder is talking to another agent next to an ambulance and it is shot at night despite it being morning only a couple of seconds ago. (00:33:53)
Continuity mistake: Scully pushes Pfaster into the bathtub and he gets out soaking wet however when he leaves the bathroom and begins to chase Scully around the house his clothes are bone dry. (00:41:20)
Revealing mistake: When Mulder, Scully and the other agent are looking at the covered body of the dead prostitute if you look closely you can see her chest rising and falling. (00:17:22)
Revealing mistake: During the opening funeral scene if you look closely you can see the dead girl breathe. (00:02:28)
Revealing mistake: When Scully makes a purchase at the grocery store, shortly before she scans the metal fragment, the clerk gives her the total of the sale, however, shortly after the camera captures the register, which displays ‘no sale'. (00:41:30)
Answer: As he stated many times throughout the series, Mulder needed Scully to be sober and skeptical. Whenever Scully's skepticism wavered and she started questioning her own rationality, Mulder would try to restore her sense of skepticism, because he needed her to be clear-thinking.
Charles Austin Miller