Are you on cash accounting? Do the payment and invoice dates fall in the same quarter or does the payment pre-date the invoice? If the payment is in February but the invoice is dated in March (or whatever quarter dates you’re submitting for) then it might be that it’s treating the pre-payment as subject to VAT and things will even out in your next return.
I explained how the VAT estimation on pre-payments works in another post a couple of days ago:
You might find you have more success if you tag the money in as a pre-payment (“pay down multiple invoices” but then don’t assign it to an invoice) and explicitly tag the payment as 0% VAT, then go to the invoice and log payment → apply from credit.