I am just running our VAT return from the last quarter, but when I download the excel calculations, it is showing purchases from between Feb & Sept 2016 in amongst the correct ones. The only correlation I can see is the QF Receipt numbers which seem to run in order all the way through.
As you mentioned the invoice numbers seem to be in order, I would assume that they’ve been inputted recently, since your last VAT return. As they would normally be included on a return but have only just been entered, they wouldn’t have been included in a previous return as the system wouldn’t have known about them.
To ensure they’re not missed from reports to HMRC, we would include them in the earliest possible calculations, which would be this return.