Continuity mistake: In the scene where the Riley Animal Hospital sign lights up, the time comes across the bottom of the screen saying 6:21 p.m. The scene then cuts to inside the animal hospital. However, the clock inside does not read 6:21. It reads somthing roughly before 6.
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.
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").
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.
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.
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.
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.
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.