I wouldn't see this exact problem myself, but I have seen something similar. When booking, if I try to pre-allocate seats during the booking process that is what the booking engine shows for the Comair flights. I always have to go back into MMB after completing the booking to pre-allocate seats (and have therefore got into the habit of not picking seats during the booking process).

It sounds possible that whatever makes that happen is also happening to your booking. In your shoes, I would phone to do it. Check what the seat map says first, though, so you know what's on offer before you call. On Comair, it is worth doing this to get an AC pair (or one of them) if you can, whether as a singleton or as a couple - this is because Comair still has 2-3 in CE on (most? all of?) its flights and it uses the E seat.