In game 4546559, decision index 115 (markus), I'm in my buy phase having 2 coins, 2 debt and 1 Fool's Gold in hand. I'd like to repay the debt without playing FG in order to buy Alms afterwards. But clicking either "2 Debt" or "1 Debt" or "Alms" or "Copper" always plays the FG, making it impossible to get the Alms effect.
You have to manually turn your coins into virtual money first. There is a scoll-bar and a button right under or above the "pay debt".
They were not coin tokens but "virtual money" from Goons.
I can confirm that this behavior happens as well when I reload that game.
OTOH, in general the game does not autoplay 'needless' treasure if the coins already accumulated are enough to play off the debt, e.g. game #4571553, decision 89 (Ingix' turn). 2 debt left from buying Engineer last turn, 2 coins generated by Militia this turn, 2 Coppers in hand. Clicking on "2 debt" will pay off the debt from the 2 coins already accumulated; the 2 Coppers in hand stay there.