I have heard that high bator temps can cause the curly toes, but hadn't heard that about the beak. I only have one though, but maybe it was more susceptible.
It probably isn't anything to do with the incubator or nutrition. It could be genetics or just a twist of fate- a simple mutation. It should be destroyed or at least never allowed to breed as it could pass on the mutation. Hopefully its the last one you will have.
I have a buff silkie pullet i got from Ideal that has a crooked beak. I think it has alot to do with genetics. Because they do not breed for quality but quanity.