But you're responsible for your bugs, so it's their job to offer easy refunds in that case.
So I guess they now need to consolidate their payments received (likely via a payment provider) with their own system to see if this or any other orders are inconsistent.
They should refund the OP, and I suspect we'll see them do just that. But they also need to both fix their front end but also add automated systems to consolidate payments with orders to see if they match.