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Then I am guessing the egg position is why you are seeing the embryos where they are, and it is probably not going to cause any trouble.

I would probably not worry. Are you incubating the eggs upright, or laying on their sides? When I incubate chicken eggs on their sides, the embryo always seems to be on top of the yolk (as if it floats up after each time the egg is turned.) But if you incubate them upright, "up" would be near...