I've never experienced that problem, but if I had, I certainly wouldn't breed for health reasons. Unless you can trace the problem to an incubation glitch, I'd assume it was genetic, and try to trace the problem to see which parent to remove from the breeding program.
Sometimes there are 2 embryos in one egg but it's not too common. If the egg was super large when she laid it, it is probably just stuffed extra full, nothing to worry about (most likely). If it increased in size over hours or days, it suggests too much moisture in the subtrate. It could lead to a problem, possibly kill the embryo from the excess pressure inside the egg.
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