The answer to this question almost always relates to dates.
Are you on cash accounting? And if so, when did you pay for this purchase?
On new accounts QuickFile defaults to cash accounting for VAT, where the correct vat quarter for each sale or purchase is determined not by the date of the invoice but by the date of the associated payment or payments. If your quarter runs to the end of April, say, and you have a purchase invoice dated 29th April but the bank transaction tagged as the payment for that purchase was on 2nd May, then you reclaim the VAT on your May-Jul return, not your Feb-April one. This is the quid pro quo of cash accounting - while you don’t have to pay over your sales vat until your customers have paid you, you also can’t reclaim purchase vat until you have paid the supplier.
If you’re actually supposed to be on “traditional” accounting using the invoice dates then you configure this in the VAT settings section on QuickFile where it’s called “accrual” accounting mode. In that mode you will pay & reclaim VAT on all sale & purchase invoices that are dated within the quarter regardless of whether or when they were paid.
In answer to your question, yes I am on cash accounting (in VAT settings, I have selected Cash Accounting).
I am doing an old VAT return for quarter 01/09/22 to 31/12/22 which I have not yet submitted (long story!).
Most of the transactions in this quarter are things link bank charges, interest paid or some inter-company director loans. Not many transactions which I have added via ‘New Transactions’ in my bank account on Quickfile.
In this period, there was one legitimate VATable transaction from my accountants. This was dated 02/12/22 and I entered this via the purchases tab. I paid this out as well on the same date 02/12/22.
I know most of the other transactions in this quarter would not be VATable and should not be on the VAT report, but this is definitely VATable and should be showing and we should be claiming back this VAT amount.
If you’ve already submitted other (later) returns since you entered this data, then the purchase will already have been reported to HMRC on one of those - when you prepare a return in QuickFile it will include all payments for sales and purchases that are dated on or before the end date of the period you’re submitting that have not already been accounted for in another return that you’ve already completed.
This is by design as it means that if you submit a return and then later find missing items that should have been included, you can enter them with their correct dates (during the already-submitted quarter) and they will be reported to HMRC at the first available opportunity - no need to either make manual adjustments or enter the items with the wrong date to make them fall in the later quarter. But it also means that you must always submit your returns in strict chronological order from oldest to newest.
Check the exports from your other submitted returns, is the accountant purchase already included in one of those?