It has happened on occasion, usually when the aircraft has changed, but not repeatedly. I know some online check in systems can be a little confusing tho, there was one, can't recall which, it was a couple of years ago, where I was asked to 'select a seat' even tho I had preselected when I booked. It transpired, after a couple of minutes of confusion that I still had MY seat, but it was giving me the option to switch that to another available seat, it just really wasn't clear (my seat number was on the screen, but I had to scroll down to see it, hence my confusion). I like the ones that show clearly, in a different colour 'hey this is your seat right here' versions much better! Could that be the case?