I don't really know the genetics for it, if it is a genetic issue at all (which I suspect it is a recessive trait), but I know that I had a problem several years ago with a high incidence of cross beak. It was after I had brought some outside birds into my flock and had merged the new stock with my old stock (big mistake!). I ended up culling that entire line and going back to my foundation stock and haven't had cross beak since. I hatched out between 250-300 chicks last year and I didn't have a single case of cross beak.
Now, we don't want to talk about leg stubs.
Leg stubs? Short legs?