Put me on my nerves when this happens.
I don’t remember if it has been discussed before but, from what I have tested, this happens because on the world map, once you select your destination, initially the winds are not loaded correctly. The algorithm assigns you a rwy that is not based on the actual weather. The solution to this problem is to zoom into your destination airport. This way, the simulator loads the correct weather and assigns you the correct runway.
But, if during the flight the weather changes, and therefore also the active runway, ATC will keep the one selected on the world map as active. So when listening to ATIS, it will indicate that both runways are active, causing the problems with the AI that we all know.