Continuity mistake: At the end, Scully is talking with the OPR people. Her suit is dark blue like in the first meeting. The next shot she goes out to meet Mulder. She is wearing another suit. That one is a different cut and is a very dark green. (01:50:10)
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.
Continuity mistake: When Mulder and Scully stop by the fence after chasing the tanker trucks in Texas, Mulder takes out a map, opens it then folds it and looks at it closely. The map looks folded differently in the two subsequent shots, then is shown wide open again in the third shot when Mulder starts folding it again.
Revealing mistake: Near the beginning as the helicopter arrives to take the boy away, a man steps on a tumbleweed. The weed bends as he steps on it, and it is flat. It is a prop.
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.