Bear in mind that if a customer pays you twice, then the value for VAT remains as the original price, so the second payment is out of scope of VAT.
Ethics of course dictates the overpayment should be returned. If the monies are kept and offset against future orders then they become ‘consideration’ for VAT purposes and VAT becomes due.
There are also a couple of cases based around parking charges.
A first tier tribunal has ruled that extra monies paid into a ticket machine (let’s say the charge is £2.40, but you only have pound coins so pay £3.00) have no relation to the service provided and are therefore not liable to VAT.
However this is different to an ongoing case involving NCP where payment is made at the end of the parking session