Ummm...Eric, we're not allowed to swear! You might want to edit that post. Family friendly forum and all.
To answer the question, Deformities can be cause by the incubation process. I once had my temp set at 98.5 on a forced air and everything that hatched had problems. They hatched 3 days late and 1 didn't have thigh muscles so it couldn't stand, another got wry neck within 2 days of hatch....you get the idea. I adjusted the temp and the next hatch was perfect. (my eggs from the same breeding group so genetics were the same)
However, deformities can also be caused by genetics. Cross beak is one that can be passed through genetics. I've read that wry neck can be caused by poor nutrition in the parent flock. (wry tail in ducks can be passed through breeding)
Then there are things like genes you shouldn't cross. Like with frizzles and sizzles. Only 1 parent can carry the frizzle gene, the other can't.