What can I do if I had a check returned while there WERE sufficient funds to cover it?

I made an online payment as I usually do, using my Bank of America account, with more than enough money to cover the payment. I have just received notice that the check was returned, and am being charged for the return fee, as well as a late payment fee to go with this. What can I do? Will the bank refund the debt incurred as a result of their carelessness (as it was not my fault, there were more than enough funds to cover the transaction).