A phrase/idiom for : Slightly bad in something which was almost good
Idioms may (or, or at least, carry the risk that they may) make the little spotty part seem more significant than it sounds it was. Two that spring to mind :
Fly in the ointment
Curate's egg
If you want to make sure that the problem isn't overemphasised, I'd be inclined to avoid idiom :
I would have picked a different colour for the table cloths, but the dinner was excellent.
But others might think of some idioms that read as less critical.