This is indeed frustrating, especially since they take no responsibility for their part, and their fees compound the situation exponentially (i.e. after you have the fees on your account, you are likely to have other transactions in the works that will also then overdraw, while they probably wouldn't have if it weren't for the fees).
This happened to us 1.5 years ago. My grandmother died, we flew down. DH used the debit card for everything and since it was accepted each time, figured there was money in the bank (he wasn't really thinking). We came back home and had a notice of 9 overdraws at $25 each - $225. Some of those were for $5 transactions.
We didn't contest it because DH really wasn't thinking, but I feel very angry that they would accept each of our transactions. Checks are different, obviously, but the idea of running the debit card through the machine is so the bank can give a green light or a red light to the transaction. They happily accepted every one of our transactions while overdraft fees piled up and our account plunged deeper and deeper into the negatives. To me, that is immoral and unethical. The charges should have been declined. Not to mention, does that mean if our debit card is stolen, a theif can steal far, far, far more than we even have in the account? Is there any limit?
DH now only uses the CC for purchases.