The difference is that since they are backed by your bank account (rather than a running balance that you owe the credit card company or bank), the money comes directly out of your bank account. Depending on your bank's policies, even an immediate refund (with no fraud involved) might take a couple of weeks to credit back to your account. So, sure you might be made whole again in the end, but you are still out the cash in the meantime.

That may or may not matter to you depending on your financial situation, but it's probably much better to be in a position where you are debating/challenging what you owe rather than what someone else owes you.

Note: I know that the mechanics are slightly different when you "run it as a credit card" rather than a debit card, but you may be in the same boat if the money has already left your bank account (unless Visa or MasterCard lean on the bank to make things go faster in such situations).

Rather than losing credit against your credit limit, however, while awaiting resolution by your bank one would be out actual cash. Credit card companies act like actual cash is more valuable than credit - lower cash withdrawal limits, higher interest - and I'd agree.