To give you the right amount of information, may I know what specific error you're having when trying to file vat returns in QuickBooks? By this, I'll be able to review and check for any ongoing investigation for the specific error or issue if there's any.
For now, you can try filing returns using a private browser. Sometimes, the stored cache of the regular browser you're using may cause unusual behavior while working with QuickBooks.
To save you time, use either of these keyboard shortcuts:
Mozilla Firefox: press Ctrl + Shift + P
Internet Explorer: press Ctrl + Shift + P
Safari: press Command + Shift +N
If you're able to file the returns successfully, go back to your original browser and clear its cache to start fresh. Also, using other supported browsers can help us narrow the cause of this behavior.
Also, feel free to read these articles for more details about submitting VAT returns in QuickBooks Online: