It's amazing what kind of programs can be loaded into a computer to do a scan every now and then for conflicts that flash on and off on somebody's screen. Doesn't mean they will act on it except where it uses up high value seats.
I've had some similar experience some years back where I purchased separate tickets on a different operator between my originating city and a high value longhaul in first. In another case the longhaul operator called me a week before the flight and asked how I was getting to his gateway and if I wanted to keep his flight.
In another case I showed up at an European first class club after arriving on a separate ticket on another airline. The club wouldn't let me in until they confirmed my space was still available as they had written me off as a likely no-show..