Of the four KTM's I have owned I've never once had a problem getting the air filter seated properly. Although I have seen a freshly rebuilt sx150 engine get destroyed within 3 hours of riding because he didn't put the filter on properly, so I guess you could put them on wrong but if you take care when refitting the filter you should be fine.
Actually been wondering how hard it would be to put a KTM rear end on my CR5. It seems like a pain in the ass now having to remove the seat all the time just to change the air filter.