When Mulder and Scully are running around the southwest US, it's obvious that it's the middle of summer. When we see Mulder in Antarctica, (in the SOUTHERN hemisphere) the sun is out. If it IS mid-July or August, Antarctica should be in the middle of a LONG winter. [Antarctica does not experience a total lack of light during the winter as the Arctic does, due to the tilt of the Earth. The shortest days in Antarctica are in June. In July, there are varying hours of light, usually around 5 to 6 hours, increasing as the month goes on. Around the middle of July, the sun is above the horizon, but even before that, there is light enough to compare to dawn in the Northern Hemisphere.]

At the end Scully is wet and half clothed in the Antarctica - wouldn't she die of hypothermia? [Not necessarily, because many people have endured more extreme forms of exposure than she did, and survived.]

At the end, when Scully is talking to the board of FBI members, she is not wearing lipstick, a second later, when she meets Mulder on the bench, she is. [She could have had lipstick in her pocket, and put it on right after the meeting. You know how women are about things like that.]

Near the end of the movie, after Mulder rescues Scully from the spaceship, Mulder's artic cat had run out of gas, so how did Mulder and Scully get home from Antarctica, with no vehicle, and no one around to help them? (This is of particular interest because of an incident which occurs during an episode of the 8th season of the X-Files, entitled, "Alone." This episode aired a couple of years after the movie was released. In this episode, there is a character, Agent Harrison who appears in only 2 episodes of the show, the first of which is this episode. She is a fan of Mulder and Scully's and at the end of the episode she asks Mulder and Scully the very question that I ask above. Instead of answering this question which seemingly would not have an answer, Mulder and Scully argue about whether or not it was a spaceship and this is how the episode closes.) [Mulder is not stupid, there are several ways they could have made it out. Just because the gauge reads empty does not mean Mulder does not have more fuel in cans inside the Cat. He might have run out of fuel and was close enough to the coordinates that he figured he would refuel after finding Scully. He might also have a radio or satellite phone to call another Arctic research station for a pickup.] Corrected by Grumpy Scot

During the film, the main characters figure out that the virus is transmitted via the bees, who get it from the corn.  The problem is corn is wind pollinated, not insect pollinated. The reason they had a corn field is that they needed added suspense by having the main characters run through the field. (It would look silly running through a field of squash). [Both the corn and bees are genetically engineered. Normal pollination cycles don't apply.] Corrected by Grumpy Scot

At the beginning of the movie, Mulder tries to get a soda from a vending machine that seems to be fully operational with the front panel lit up and everything, but when the machine doesn't work, he looks behind it to see that it is unplugged. If the machine was unplugged then the panel light would not be lit. [It's plausible that the machine was lit up via battery operation. If the machine has been tampered with to include a bomb, then it could have had a battery circuit installed to give the impression that it was fully operational without actually having plugged it in. Kind of the point.] Corrected by Chimera

After Mulder rescues Scully, he gives her his coat to wear as she is naked. When they come out of the cave, you can clearly see that Scully has white socks on. Where did they come from? [He took the ones the aliens took off her and left on the glass coffin-like bed they brought her in. Same thing goes for her trousers.]

How did Mulder find Scully out of all the thousands of bodies taken by the virus with the tanks frosted over too? [In a few scenes before he finds her, he spots the coffin-like chamber which she was transported there in, which, according to the actual X-Files movie script, is "a man-made object that stood alone in a sea of alien atmosphere."  Mulder then looks for her nearby, because she had only been frozen for about 48 hours.]

How did they get out of the Antarctic at the end if the snow cat Mulder drove was out of gas? [He wasn't out of gas - the fuel gauge shows 1/4 full. He stopped because he was at the co-ordinates he needed. Therefore they could have used the snow cat].

You cannot vaccinate for a virus once you have it. With virus vaccinations, you are injected with a small amount of the virus and your body develops antibodies. [Apparently not true - smallpox can be vaccinated against after exposure].

Mulder is walking in Antarctica, where  the average temperature is -100 degrees Fahrenheit, and all he is wearing is a fur coat and leather gloves... [It is rarely below -20C on a summers day (which it must have been in the story given the brilliant sunshine). You can quite comfortably walk around with just a parka on if the wind is calm (admittedly it rarely is) and the sun is on your face.]