Breeders do encounter "problems" as such more than some are prepared to admit or talk about,have to say flat ears i haven't heard of in the way you describe,maybe deformity's as it were are possibly due to the age of your girl-this is where you should think about having her spayed and allowing her to live out the rest of her years as a boy/kitt ,care free gal happily wasting her day being just a cat
By the way what breed are they?