Title says it all. This baby has been culled

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If that is the only one that hatched like that, I would chalk it up to a freak accident.
Otherwise.... Temperature swings, off humidity, and nutritional deficiency.
Could it be from the baby just not forming correctly? Are some of your ducks inbred, its actually fine, until it gets to the point of the babies not forming correctly or have disorders. Like in the wild, Muscovies can tend to breed with siblings their first year because they can't find other more suitable females. But they know not to interbreed to much, unlike domestics which sadly can't tell the difference.
It was a really big yolk, and the abdominal skin would have been stretched quite thin and transparent.
Perhaps it's because I am only seeing it as a picture, but it actually looks pretty normal for a new hatched bird other than the lack of belly down (again, could just be stretched so thin it's not visible). I've had turkeys look like that soon after hatching but within hours they dry and look perfectly normal.
The face defects, though, show that something was going on and culling was the best choice IMO.