Something smells off here.

The account holder can only draw against cleared funds and the bank claims they took the return entry as being out of cleared funds?
The entry should be a deposit reversal and not treated as a payment, so the stop payment order should have been matched against the relevant cheque deposit which would still be in uncleared funds.

Are you sure this is not a situation where the account holder has applied and been granted access to draw against uncleared funds? In that case if the bounced payments arose from the account holder relying on uncleared funds, well that's the account holder's fault (and problem).

But if the account holder can only access cleared funds, the stop payment should not have caused a problem as it is an uncleared deposit that is being reversed.