Don't worry, this is just (another) bug. Prepay is the same as payment at the hotel for points earning, providing if course the hotel participates to LCAH and you booked through an eligible channel. In your case, shouldn't be a problem.
Personal advice : at check-out request the invoice including the pre-paid nights, in case you have to retro claim your points after the stay. Indeed, I noticed that in case of pre-payment, many hotels tend to deliver you at check-out only an invoice for the incidentals paid on-site.