You admit that the station ran out of gasoline. If they have black bags covering all the pumps, then it can only rate as a closed location since customers can't buy any gas at the time of your visit. The convenience store being open is not important in this context since the availability of gas is the underlying criteria for open or closed status. The respective lights being turned on is another dynamic.
Unfortunately, you caught some bad luck that the station didn't have gas to sell. I think we all get situations that are beyond our control from time to time. If it occurs on the furthest trip out from home, then it really stinks.
How do you know that they ran out of gas? Did you go inside to speak with someone or were there a signs on the pumps. I recall a station I visited that had something similar, but they did not pass a state inspection and were barred from selling gas until they passed the review.
Not that I would've done this, but I wonder if it would've been worth going inside to investigate the black bag scenario and see if you could move one bag to take some quick pics.
I think sestrahelena meant it isn't worth the time to argue it since it is time consuming. I would take the docked pay and move on.