Happened to me last week most recently. It sucks but just dispute the charges and the bank ends up having to refund everything... overdraft fees included as it wasnt you.
I just keep very very little in my checking and I don't link any of my savings accounts to my checking accounts so more money doesnt get transferred over and subsequently stolen.
Also make sure and pull your credit in a month (assuming you dont already regularly pull it) and make sure none of this ends up on your permanent record.