I know this is a bug and I hope it gets fixed, but for now I do two things.
1) I always left click stackable loot because if you right-click auto-loot a stackable item it won't show-up in your inventory if you already have one of that item.
2) If I sell a stackable item I get the money for it, but the item remains in my inventory (as already reported), but right afterwards I destroy the item from my inventory.
Doing these two things keeps me away from problems.
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