Has that always been the case for that save? I ask because disabling a mod doesn't remove the effect it's had on a save. So just making sure that we can exclude mods as having an effect on this. :)
I know it can happen in the unmodded game if some airports are too close to each other, and it can happen if they are in certain specific spots in relation to the invisible flight paths that cross the map. The easiest way to test if that's the case, would be to move the airport to a new location and see if it still happens there.