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)
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.
Continuity mistake: While Mulder climbs down the inside of the spaceship, when he enters the second hole he wears gloves but when he falls out of if the gloves are gone. (01:27:20)
Continuity mistake: When Mulder encounters the Well-Manicured Man, all doors of the limousine are closed. However, in the next shot the driver's door is open. (01:17:25)
Visible crew/equipment: Near the entrance of the building, when the fire brigade arrives, a guy holding a boom microphone is visible. (00:19:25)
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.