Many of the following continuity/logic errors were observed while I was watching FX reruns of the first season, which I missed the first time around. Bear in mind that I overlook a lot of little discrepencies, but when something's really amiss, it un-suspends my disbelief, thus breaking the spell a good story weaves.
Season One
Conduit
Jersey Devil
Ghost in the Machine
Ice
Eve
Fire
A little smoke inhalation/panic attack combo and WHAM! Right into a coma. Mulder's not very tough. But he still looks cute!
Season Two
Ascension
Humbug
The angle of the nail Mulder extracts from Dr. Blockhead's nose changes from one shot to the next.
Steam rises from Dr. Blockhead's giant stewpot before The Conundrum surfaces, then we no longer see any steam. Come to think of it, how long did that bald-headed, jigsaw-puzzle tattooed naked guy have to hold his breath? Oh, well. That was the episode that won my heart (and the first script from that God, Darin Morgan) so I can forgive any and all discrepencies in an otherwise genius episode.
Season Three
War of the Coprophages
Pusher
Season Four
Sanguinarium
Gethsemane
Season Five
Warning: Spoilers for various X-Files episodes contained below.
Squeeze
Scully -- off camera -- gets suddenly taller and shrinks again for her closeups!
In this second episode, while Scully is trying to convice Mulder to leave the case alone -- that it belongs to her old colleague (who had asked for help) -- she's saying, "Mulder they don't want you involved, They don't want to hear your theories. That's why Blevins has you hidden away down here." At her imploring, Mulder has stood up and he says, "You're down here, too. Look, why don't we agree to this. They have their investigation and we have ours. And never the twain shall meet. Agreed?"
During this exchange, in David's closeups, is eyes are straight ahead, surfing at least six inches above where the top of Scully's head should be. Yet, in Gillian's closeups, she is her normal height, with her eyes cast upward.
Similarly, in Conduit, Scully suddently gains 3 inches from one scene to the next.
In the FBI regional office, from discussion of the Brandenburg Concerto to the scene where the mother yells at our heroes in the corridor. First, Scully barely rises above Mulder's shoulder, then she's nearly as tall as he is.
Who put the foliage over the bare buttocks of the dead Beast Woman? Oh, yeah. The censorship department, of course.
So many computer errors! Too many to enumerate. A few favorite nitpicks from this one:
One nice touch: "What are you doing, Brad? ... Brad, why?" seemed kind of silly at first, but was a nice reference to Hal in 2001.
All those in favor of the FBI asserting its authority to hold Bear until he's sufficiently quarantined, raise your hand.
Digitalis is extracted from foxglove, not the other way around.
So, if Mulder is so afraid of fire, why did he run upstairs alone to save the children? Would Scully really let him go by himself?
Duane Barry
Why is the security guard at the mental hospital carrying a gun? Even guards in jails and many prisons never carry guns.
Silly lighting discrepancy
When Mulder finally catches up to Duane's car, it is dark and raining out. Mulder pops the trunk and looks inside for Scully, or any evidence of her presence. While I understand unexplained light sources in otherwise dark places are necessary to film night scenes, here we clearly see a spot like a flashlight scanning across the floor of the trunk. Mulder is carrying only a pistol. It would've been so easy to put a flashlight in his hand. It's at least conceivable that he carries one -- even a penlight -- in his pocket.
The Blessing Way
Any therapist would know better than to touch a patient during an emotional moment. In fact, most would never touch a patient at all, unless perhaps the patient requested the touch. For Scully's counselor to touch her when she was recalling a traumatic moment, especially when her eyes were closed and she was not expecting it, would not only be unprofessional, but unbelievable. Of course, she snapped out of her reverie and stormed out of the office.
OK, so Mulder has this sort of photographic memory,
yet he doesn't remember what kind of bug hit his windshield in Massachusetts. The cop asks, "Cockroaches?" in an alarmed manner, reaching for his gun. Now, that would be really unlikely on a car windshield, yet Mulder says, "I dunno, maybe beetles. I'm not really good with bugs." You'd think Mulder would either notice that it was a grasshopper he had wiped from his windhshield, or at least know enough to say it wasn't a cockroach, which logically he should've known wouldn't jump onto his car in the middle of night.
Dr. Berenbaum, "Bambi," carries a badge? Since when do USDA officials carry badges with gold shields in their back pockets?
The robotic insects created by Dr. Ivanov don't walk on their six legs, they roll on wheels. The legs are purely cosmetic.
If there were an error as Mulder was typing his report onto his computer, he wouldn't be able to correct it by smacking the terminal. But we all know that, don't we?
On the other hand, I really loved this episode, and you can see how much I loved it at my 50 Reasons to Love Cockroaches page.
The case of the amazing moving warrant
When the cops bust in to arrest Modell, Mulder slaps the warrant onto the TV screen -- a TV that is showing a Svengali movie (cute!). At first the warrant is upright, but in the next shot it's cocked at a 45-degree angle.
Home
OK, I know the angents are in a hurry to save the "victim" here, but ...
shouldn't they at least have notified the state police they were about to raid the Peacock house? Assaulting a home is one of the most dangerous operations a police agency ever undertakes. They needed backup. And while we're on the subject, Scully asks, "Is this vest really necessary?" Pardon me, but we know these boys have already killed two adults, the agents believe the Peacocks are holding a kidnap victim and have ample reason to believe they would likely go out of their way to protect their home.
Speaking of the raid on the Peacock house, why did the sheriff's deputy go in first? In a small town such as that, he would not be adequately trained to raid a home. FBI agents are.
Snow sure is a localized phenomenon in Illinois.
Scully and Mulder are standing in the door of Dr. Franklin's home, and while their hair is dry, it appears to be snowing in the yard behind them. They're not carrying an umbrella as they often do, either.
Scully was bleeding from her back when she fell down the stairs, but not from her nose, where she had been bleeding unprovoked for the last six TV months. Also, how can a woman with advanced, metastasized cancer run after a suspect -- particularly after being thrown down a flight of stairs? Surely, she must be weak and in pain.
Detour
More weather oddities ...
After Michelle disappears, after the commercial break, Mulder comes running to Scully's aid. His hair is wet, presumably from rain. Cut to Scully, spinning intensely and holding out her pistol. Her hair is dry. Mulder runs up to Scully, and lo and behold, his hair has now dried.