Factual error: Dallas, Texas is not surrounded by desert mountains. This is a dumb tourist mistake; when that shot of downtown Dallas appeared on the screen audiences there groaned in unison. (00:07:30)
Factual error: The stamp of the scene says that it is Wilkes Land, Antarctica. Wilkes Land extends from Cape Hordern in 100°31' E to Pourquoi Pas Point in 136°11' E. However, the coordinates of the spaceship are 63°00' E, 83°00' S, so this place is located definitely outside the area of Wilkes Land. (01:24:00)
Factual error: When the Smoking Man comes back to the base, in the first shot the tracks are shown, but they definitely do not belong to his snowcat but Mulder's. Only Mulder's snowcat has triangular-like shape of the tracks. (01:33:05)
Factual error: North Texas was never covered by glaciers. The glaciers never got south of Kansas. And there weren't any mountains in Dallas then, either.
Factual error: The two human hunters shown in "North Texas - 35,000 B.C." look to be Neanderthals. Neanderthals were strictly Old World. There may have been early Native Americans around Northern Texas then, though generally it is assumed that the Settlement of the Americas had not yet taken place or was in its very early stages.
Chosen answer: If they had put an "Out of Order" sign, or left it unilluminated, someone in charge might try to have it fixed or replaced, or could have checked to see if it's plugged in, etc. By leaving it illuminated, it doesn't look out of place and simply not taking money wouldn't arouse too much suspicion. In my own life, when I've come across a seemingly working vending machine that won't take my money or dispense drinks (but gives my money back), I just find another one instead of calling someone or reporting it. But yes, it is very convenient to the plot that Mulder just happens to try and use this particular machine.