I had this happen last year, they only got about $200.00 before I caught it since I check my accounts daily. I'm pretty sure it happened at a Panda Express since the cashier takes the card to swipe it.
Dispute process worked, the bank put a temporary loan in my account pending resolution. The loan then converted to replacement.No fee.
The banker who helped me with the dispute suggested that I open another checking account that is not tied to my overdraft and only keep a small amount in it. I can do this for free too.
So far it works great. If I'm going out, I transfer some money to it and transfer the remainder back when I get home. I put several hundred on it when I went to Prescott for gas and possibles, put it back when I got home.
Or I can transfer to and from with my Droid at any time.
And I don't go to Panda anymore. I sent them an e-mail to their corporate and told them I would not patronize their restaurants until they set up a system where the card does not leave my hand.
That's now my policy: My debit card does not leave my hand. (Except for ATMs of course where it sucks it in til the transaction is complete).