I think the possibility of getting a duplicate of a stack of cards you already had is way too strong and should be reserved for an incense effect
Had you already burned through your first stack? It shouldn't let you add a card to the shop that's already in there unless it's out -- if it is, that's a bug.
Or are you just saying that overall, having more than 5 of a card is too strong (depending on the card)? I was thinking rarities would mostly take care of that, and the occasional OP run seems fine, but maybe it's too much.