Its been pulled in to the VAT return because you are on cash accounting. The fact you are on cash accounting is exactly why its including them. Cash accounting is accounting for VAT “when” you receive a payment.
Regardless of whether the invoice was issued In October, the fact you were paid in November and on Cash Accounting, means you are charged VAT on this payment by QF.
However having said this, as you were not registered for VAT in October when the invoice was issued, providing the “supply” took place in October, and not November, you can adjust your vat return to remove the invoice which is being included (im guessing you will need to manually calculate the invoice total less VAT and adjust the net sales and Sales Vat boxes. If however you are using Making Tax Digital, then someone else will need to explain how to adjust that as im unsure.