Creating a new VAT return the figures no longer autocomplete, and can’t be entered manually except as adjustments, which then no longer file. Signed up to MTD February 202 until current VAT period (1/3/21 - 31/5/21). HMRC links appear to be functional.
Are you generating your VAT return from data you’ve already entered into QuickFile or are you creating a VAT return from figures you’ve calculated elsewhere?
If you are cash accounting it may be that the payments allocated to the invoices are outise of the VAT period - I would recommend checking your payments
If you are on cash accounting and the payments were made/received outside the relevant quarter then there’s nothing to correct - the VAT isn’t due until the payment date.
Or do you mean the payment dates recorded in QuickFile don’t match when the money actually changed hands?
Can I check - The invoices that I have generated during the VAT period 1/3/21-31/5/21 and have been paid in the first week of June 21 means that I do not owe any VAT for that Mar-May period? IF that’s the case will the next VAT period (1 June 21-31 Aug 21) reflect these invoices?