I regularly used Bank of America bill pay some years ago but stopped when I got burnt a few times just as the OP did. Once, I don't recall the payee, I was able to get them and a BofA rep on the phone at the same time. The BofA rep acknowledged the time the payment was set up for so the payee went ahead and waived the late fee. It was a lot of hassle though, so I simply stopped using the BofA bill pay and pay directly via the vendor's site whenever possible. This includes two different Citi cards, including my AA card. Citi counts it as paid once you do that even though the money may not be debited from your bank account for a couple of days.

The only exception is one vendor who charges a fee even for bank debits on their site, so I still use BofA for that but the amount is tiny and I pay it well in advance.

I hate auto debits, whether from a CC or bank account, and will use them only if I have no choice or there is a significant savings involved.