Hello Justindayservice
Thanks for reaching out to the Community.
To understand why this is happening we would really need some screen shots. If you could go to taxes and then hit on prepare return and attach a screen shot of the boxes 1-9. Also if you can go to reports>search for the vat detail report and attach a screenshot of that for quarter you are looking to file and we can have a look at what may be causing this to calculate in that way.
Thanks
Emma