Game #949336 on oregon. 5 player game with Mountebank, to explain how this happened in the first place.
I played a Butcher, trashing a Curse when all Curses and Coppers were gone. I believe I should have the option of paying 0 coin tokens, and failing to gain anything. Instead I was forced to spend 2 coin tokens to gain an Estate. I didn't have an option to try to gain a Copper or Curse from the empty piles.
This is a case where a very good interface (letting you click on the card to gain directly and deducting the necessary coins automatically) can backfire in a rare case.
My suggestion: The game needs to figure out anyway which cards are gain-able with the available coins. Let it do the same with an assumed coin count of zero (that is, find out what the trashed card cost and find all the top supply cards with a lesser or equal cost). If the latter turns out empty, then present the user with an additional option "Don't spend coins and don't gain a card".
This way, the current intuitive interface is not changed in the overwhelming majority of cases, and edge cases like this can be handled with just a simple option.
What would have happened if estates had also been out?
I tried this and could make it work in game #1056956 on tokyo.
The game continued correctly: I trashed a copper, nothing happened as I could not gain any card with my 2 tokens and I went to my buy phase.