If the VAT return does not contain data you are expecting to see or, the amounts shown on within the individual boxes are incorrect, it's likely that when running your VAT Return you may not have booked all of your transactions within the period selected so some could still be in draft. If this is the case tick the box Include non-booked entries when running your return you will then see all booked and draft entries.
When your return appears you will see a message top left that the report contains unbooked entries. The can be checked by clicking on the amount to the right. You can also check which vat code you have entered making sure these are correct and appear in the correct box. If the entry has been booked with the wrong vat code you will need to reverse the entry to correct and then create or copy the entry and change the vat code. You can make the corrections in draft mode, run your report again to check you have made to correction correctly and then book.
Another area to took should for errors is Show direct entries, this will show any entries that have been booked directly to your vat account within the chart of accounts without a vat code. When an entry is booked this way it will not appear on your vat return. The system will give you the option to enter show you a vat code by clicking on the drop down, select the appropriate vat code and save. The entry will then appear within your vat return.