If Auto Pay works the same as Dartford Crossing, then it's your responsibility to keep your nominated vehicles up to date. I know through recent personal experience when I was alerted to a debit because Dart Charge notify the account holder whenever there's a transaction(otherwise I'd have remained in ignorance). I did the same as you and was given the same response. I've chalked it up to experience.
I thought TfL did something similar by notifying account holders, whether per transaction or per billing cycle, that debits had been made.
Your description doesn't refer to how you found out, but IMO it's important. For example, if TfL send you regular billing updates which you missed then there's a reason for this.
