Continuity mistake: When Mulder and Scully are moving into the house, there is a shot of Mulder's watchface which reads that the date is the 7th. A few minutes later, Scully is walking around with a video camera, and narrating and she says the date is February the 24th. (00:08:35 - 00:09:30)
Factual error: In the scene where Daryl Mootz pulls up in his SUV for the rain-making event, there is a shot of the SUV with a front Kansas license plate. Cars in Kansas only have rear license plates. (00:12:55)
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.
Continuity mistake: When Frohike plays the slot machine, the first position on the reel shows a single bar. After Byers spots Suzanne, the camera goes back to Frohike and the first position now is not a single bar. There wouldn't have been enough time between the shots for Frohike to have another pull of the machine. (00:10:15)
Continuity mistake: During the conversation with Scully regarding Wayne Weinsider, Mulder says "I don't know why. I'm not a psychologist", which must be a big surprise for all viewers, to say the least. Mulder graduated from Oxford University with a Bachelor of Arts degree in Psychology (e.g. "Dreamland II") and he worked for some time as a profiler for the FBI (e.g. "Young at Heart"). (00:32:25)
Continuity mistake: At Mulder's 'funeral' around when there is a knock at the door, we see Frohike raise his bottle to take a swig. The shot cuts to facing Scully and we can see Frohike further in the background and his bottle is nowhere to be seen, when he should've been mid-swig.
Character mistake: Scully continually addresses the senior police officer as "Captain." But he wears sergeant's stripes. As a law enforcement officer continually dealing with other law enforcement officers, Scully is not likely to make this mistake. More likely a failure to match script with costume.
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.
Other mistake: This episode establishes that whenever Pinker Rawls passes through solid matter, his clothes remain behind, as anything he is wearing does not share his ability. However, late in the episode when Jackie throws the pot of boiling hot soup at him, the soup is shown to completely pass through his shirt, when it should have stuck to his shirt instead.