If a transaction has been intentionally or accidentally marked as excluded for a VAT return, it will not be picked up when creating a VAT Return.
If this transaction then needs to be included in a VAT return it can marked as included in following way
Click Nominal Ledger then click Processing.
Click VAT Return Exclusions.
Find the transaction in question then untick the check box at the end of the row.
You're then prompted to confirm that this allows the transaction to be picked up on the next VAT return.