No matter whose shares fall short, whether it's marketmakers, shortshooters, etc. there's an imbalance on shares cleared in the market.
Looking at the following chart, you'll see where 25% of shares traded today had not closed out their position.
As to where those shares are domiciled can be anyone's guess, but because they haven't been settled by the DTC into the "buying" parties' accounts, a short balance is recorded as a result.