When this happens, it's usually because the hotel accidentally charged the guest the internal reimbursement rate that should have been charged to HHonors. Most of the time, contacting the hotel will get it fixed right away.
It's more likely that a change to the reservation happened such as number of adults or the specific room type - either an upgrade, or guest requested a different number of beds or whatever - and the system tried to reprice the reservation. The person making the change is supposed to override the rate to the original rate - which for all points stays should be $0.00 - but accidentally selects the new rate, which will be the best available rate for that night. It's unfortunate human error, but should be easily corrected by the hotel if that is the case.