I've hatched a few call ducks, and I've had a couple die in the process of hatching, but I didn't notice any obvious deformity. Your case may just be a fluke. If it should happen to another from the same parent stock, then it could be a genetic flaw that you'd want to avoid.
Freak accidents happen, even when you are doing everything right. Some problems can be caused by a lack of certain vitamins inside of the egg. I put my duck for hatching eggs on a supplement. Sorry for your loss, don't give up.