If a payment has been dishonored by the bank you will need to click on "Dishonor" on the bank statement screen against the funds debited.

This will bring up a list of all payments made to the account for the same amount, click on the appropriate payment to dishonour.

The payment will be reconciled, reversed and dishonoured.

If you can see both the deposit from the tenant and the dishonour withdrawal on the bank statement, receipt the deposited funds first, and then dishonour.