Once you authorised QuickBooks to interact with HMRC, make sure you've received an email confirmation from them. Since, it takes 72 hours after you have selected MTD on the HMRC's website.
If you've already received the email and all information is correct, this could be a web issue. To start with, open QuickBooks Online using an incognito window. This is the best place to isolate web issues. From there, try to submit the VAT return. If you're able to do so, go back to your main browser, then clear the cache. It's advisable to clear them out to avoid unexpected website behaviours.
Moreover, using a different browser can fix issues like this (Google Chrome, Internet Explorer, or Mozilla Firefox).
Get back to this thread if you need more help. We're just around.
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