As I said, I don’t understand what they were doing. Why take card details if you don’t know how much it is and you need a manual calculation.
Or are you saying the manual calculation was done, you called to pay, and it was then sent off for ticketing? Usually if it runs out of time due to cvv dropping out it doesn’t result in cancellation. It is a confirmed booking, but just not ticketed and ticketing can take place later when you/ba pick up that it hasn’t been done. All sounds quite odd.