First time I booked a prepaid rate I had a long discussion at checkout with a supervisor and eventually also the manager because they wanted to charge me (again). I assumed it was already paid because it was a prepaid rate and they kept insisting they hadn't.
So I eventually grabbed my laptop and started checking all my CC receipts to indeed find out they hadn't....
So now I keep records off all bookings that have been truly prepaid and those who haven't.