Here's a list of deformities and their likely causes:
https://www.backyardchickens.com/ar...tions-and-deformities-in-chick-embryos.67021/
Is it possible the parents are from a heavily inbred line? If you aren't able to find out this information, it'd be worth bringing in a replacement roo from a very different source than you used originally to ensure there is enough genetic diversity in your flock. I believe inbreeding for one generation is considered ok, but any more than that and you may start to run into issues.
With your feed, is it pelleted or loose grain? The latter allows the birds to be selective when eating and can cause diet imbalances or deficiencies. Just like people, they don't always make healthy choices.