It's possible No VAT was selected on the Amounts are field when creating a transaction. This maybe the reason why the VAT amount isn't updated.
VAT return is based on the transactions created with VAT codes. To help fix this, you can manually open each transaction and review to see if the right tax code was assigned. If not, you can manually edit the tax code and assign it to the correct one. Here's how:
Go to the transaction you created.
Make sure the Amounts are field isn't selected to No VAT.