I think you know the answer to your question. If you're in doubt, check out Official Interpretations to section 1005.17 of Reg E, in particular the last sentence of comment 17(b) - 7 (Confirmation) --- "An institution complies with the confirmation requirement if it has adopted reasonable procedures designed to ensure that overdraft fees are assessed only in connection with transactions paid after the confirmation has been mailed or delivered to the consumer."
If this is an isolated incident, I'd likely agree the bank is generally in compliance. But when you find an isolated incident like this one, you need to fix it. And that means getting the confirmation out and, from where I sit, a refund of any OD fees collected since the error. I hope there aren't many to refund.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8