I've had a problem happen for the first time recently. I booked a ticket for myself and a companion through my Aeroplan account on the AC website. It ticketed properly with 2 flex fares that I bought but I don't seem to be the primary ticket holder on the PNR/tickets. (Checking the PNR shows my companion has a lower ticket number than I do.) I'm a 50K member and my companion has no status. I am able to apply the benefits such as complementary preferred seat selection for myself but not my companion. I ended up having to contact AC to get them to select the preferred seat for my companion.
I'm not sure if there is a fix for this but I've never had this happen before. I've tried removing and putting back my Aeroplan number into the booking but that didn't fix it. I'm hoping I won't need to contact AC again to make changes and use my benefits for the booking.