Thank you for posting, @lylew.
All the transactions that have a VAT rate will be included in the VAT return. That’ll only be removed or not included if you can remove the VAT code that you’ve added to the transaction.
To know more on how the amounts on the VAT report are calculated, check this article: VAT Detail Report.
See the following article for more information column titled Exception Amount when preparing your VAT return: VAT exceptions and reports.
Let us know if you need further help in preparing your VAT return. I'm always here to assist. Have a wonderful day!