The problem appears to be Quickbooks taking the data from the submission spreadsheet (e.g. total sales for the VAT quarter) and adding it to quickbooks as a new sale (or cost) therefore messing up the data by adding spurious journal entries.
This also happened last time I tried to submit VAT. It was even worse then, so this is some kind of progress...
Let's make sure that you're using MTD so you can successfully submit your VAT without any issues. Allow me to share a few information about this.
Starting in April 2019, all eligible UK VAT-registered businesses will have to keep their financial records in a digital form and submit their VAT returns using the approved software.
If you're still using a spreadsheet with XML files, this is the main reason why it's messing up your data.