From time to time payments from tenants may dishonour, you will need to ensure that you follow these steps to account for the dishonour 

In the bank reconciliation screen locate the payment on the left-hand side that has dishonoured then select the word "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.