Cash Manangement - Problem autoreconciling receipts

One of our clients has recently encountered a problem when they reconcile receipts via auto reconciliation within Cash Management.  Our client tried to reconcile an amount from the bank statement to a receipt batch for the same amount, unknown to them at the time one of the receipts from the batch had already been applied, so as part of the auto reconciliation process the difference from the bank statement total was applied to bank charges?  Is this standard functionality?? If so, can this be amended so any difference is left unapplied rather than applied automatically to bank charges??

Regards