I am assuming you mean GST or HST tax (principle should work in any case). When you click on the button to prepare your return, the initial report should come up to indicate there are exceptions. You can drill down on the exceptions to discover where they originate. Usually, they are transactions that have been back dated to a period that has already been filed. If you agree with the transaction and, yes, it was missed, then go back to the return and select "adjust" which will add the amount to the current return.
If the transaction was a mistake and should not have been backdated, you have the opportunity to go to that transactions and change the date to the correct one.
This should work for both GST collected and Input tax credits.