Selling certain items back to their respective stores, like runes for example. If a store has 300 runes in stock and you sell 20 runes back. The store's stock will stay at 320 instead of 300. I am not sure if the rune stock should be going back down at 300?

Pretty sure it should be.

It should go back down to store stock but this sounds more like a feature than a drawback :P

Something along these lines happens at the Ardounge general store, run only by Aehmed.  He has a decent stock of unstrung sapphire amulets for sale that never goes away.