Revealing mistake: In the end when Mulder is reading the paper in the park. The paper is clearly a prop. Only the frontpage is real - when he puts the paper away you can see that the rest of the paper consists of blank pages. (01:45:45)
Continuity mistake: As Mulder and Scully enter into the building that houses the bees is seems Mulder's tie gets blown over his right shoulder and then he is seen inside and it is over his left shoulder. (01:00:30)
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)
Revealing mistake: When the booby-trapped car explodes, the detonating wire is visible running out of the exploding car and out of shot. (01:22:55)
Continuity mistake: When examining the body of one of the four fallen firemen from the explosion, Scully is wearing a dark grey suit. In the close-up shot of her hand with rubber glove, the arm is wearing a white doctor's coat. (00:37:40)
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.