whenever you encounter a similar problem, don’t hesitate to let know the ICAO of the airport involved, in order to fix it manually. Sometimes the automatic border configuration doesn’t apply well and doesn’t cover the entire structure. sometimes also there are real enlargements of the airport it self , but if the modification is based on adding a runway, I suppose Simfly can’t “add” a runway on the map, because the simfly map is “owned” by Mapbox (maybe the issue regarding UUDD https://forum.simfly.io/t/update-airport/12200/7 ) .
But if it’s only a matter of most of the issues, and that is: not always the borders of the airport surround the actual position, then in this case Simfly can make a bigger “polygon” that will include the entire airport. This is different from adding a new runway on the Mapbox site. For UUDD , Mapbox has only 2 runways displayed.