When Mulder is locked in the room with the bomb, the person cutting through the door starts at the top of the door and works downward, but all he really needed to do was to cut around the lock and the door handle, which would have saved time.
When Scully is observing the state of the corpse in the morgue, she tells Mulder "it's completely (o)edematous" (American spelling of the word is without the o at the beginning whereas British spelling is with the o; the Bluray subtitle shows it as the British spelling). She mispronounces the word, though, saying the 'at' part as "aysh" instead of "et." The '(o)edem' part can be pronounced multiple ways, but the 'at' part is always pronounced "et." As an MD, she would know how to properly say this word.
After Scully gets stung by the bee in the hallway, Mulder rushes back into his apartment and dials 911, while through the windows you can see that it is still daylight. But when the paramedics load Scully into the ambulance waiting outside, it's now almost full dark.
As the train carrying the tanker trucks passes by Mulder and Scully, the entire train is past the railroad crossing before they even move, yet when they start to get into the car the train is passing over the crossing again.
When Mulder and Scully enter the bee domes, Mulder opens the door and is blasted by the rush of air used to support the structure, which blows his tie over his RIGHT shoulder. The next shot of Mulder shows his tie blown back and up over his LEFT shoulder; the next shot shows his tie in normal position and the next shot the tie is back up and over his left shoulder.
In the limo where the well-manicured man shoots his chauffeur while sitting beside Mulder, you can see Mulder lowering his arm while holding the vaccine immediately after the shot. But in the next scene, both of Mulder's arms were raised.
When the helicopter is flying through Dallas, it passes the "One Wilshire" building in Downtown L.A. As it lands, the building to the right bears the "Pacific Bell" logo which would not be found in Texas.
In the scene in "North Texas" where Dallas can be seen in the distance, the surrounding area is dusty, treeless desert. The real areas in Texas where Dallas can be seen in the distance are live-oak covered wooded areas or large, sprawling suburbs.
The young boys and the townspeople from the "North Texas/Dallas" area in the movie all talk with heavy accents. This is erroneous; the stereotypical southern drawl is present in people from West Texas, whereas inhabitants of North Texas (including the Dallas area) and East Texas do not possess discernible dialect from the average American accent.
When the three boys are questioned by Scully and Mulder about which direction the trucks went, they point to their right (viewer's left). Because they are standing in front of the Dallas skyline with Reunion Tower on the left, then they are south of Dallas, and are pointing west. In the next scene Scully and Mulder are driving through Texas. The shadow is on the driver's side (north side) of the car which means they are driving east.
The coordinates that the Well-Manicured Man gives Mulder to locate Scully are not in Wilkes Land. 83 degrees latitude South & 63 degrees longitude East are indeed in Antarctica but hundreds of miles from Wilkes Land, closer to the South Pole.
The movie takes place in July but during the sequence in Antarctica the Sun is up (fairly high). During July, the Sun never rises in Antartica (at least not at the coordinates given by the Well Manicured Man).
It would be almost impossible to go to the interior of the Antarctic continent in July (middle of the winter) due to extremely bad weather. Barring extreme medical emergencies, no U.S. flights land on the continent between April and October.
The film opens in prehistoric times, 35,000 B.C., in North Texas . A Neanderthal man stumbles upon what appears to be a large, primal, vicious alien in a cave. Neanderthals' habitat ranged from Western Europe to the Middle East. No Neanderthal has ever set foot in North America as far as the fossil record is concerned.
The film opens 35-40.000 years ago with Neanderthal men exploring an underground cavern. No scientific study every done suggest that human beings (even primitive ones) ever existed in the Americas prior to 18-20 thousand years ago.
And since there is a definitive trail of human settlement from what is now Alaska down to North and South America, human beings wouldn't have been in North Texas until 8-10 thousand years ago at the earliest.
Adding to the revealing mistakes in the last scene, the newspaper articles except one that Mulder is supposed to see, all have the same content beginning with "While he amended the compromise into a bill[...]".
Mulder discovers the bomb in the vending machine after noticing that the mains cable is not plugged in. Even so, the bright lights on the front of the machine continue to glow before and after this discovery.
This isn't an error, as the bomb needs an internal power supply, and the panel lighting would disguise the 'bomb', making people think it was just malfunctioning.
When Mulder is reading the article in the newspaper in the last Mulder/Scully scene (by the fountain) you can see that some pages of the paper are entirely blank - most noticeably, on the first shot of Mulder's face in this scene, and then again when he hands the paper to Scully.