I've treated it as an article of faith for some time now that when booking, to always ask for PNRs for all relevant carriers on an itinerary. Then I periodically check each of those carriers' websites to make sure that nothing has changed with my booking.

There have been a couple of occasions where something significant has changed on segments involving one carrier, and I would never know it by just pulling up the reservation on Aeroplan. I've avoided unpleasant surprises at the terminal that way.