Good point. I just checked and the Quebec Hilton charges C$20 more per night for the second guest.
Maybe one should make the reservation for 1 per room and clear it up at checkin when this is the case. You should also be aware that the spouse stays free with the HHonors guest (or was this how you got the "one occupant" rate on one of the rooms?)
By all means call with your explanation and ask for the points for both rooms.