I've never noticed it. Did it only start happening with the latest patch? I love my overlays and I'd be happy to test it out, though I wonder what could be the cause since in the end, EA doesn't see it as any different from having freckles.
Honestly, I'm at a loss as to what is causing it. These two kids were born prior to the latest update, so I don't see a connection per se. The first four kids (a single child and triplets born naturally) turned out okay, but the last couple of batches are close to an eyesore like those in the photos above plus one who has no chin, which I know to be an issue bothering many.
I'm leaning towards it simply being the in-game genetics, as they have always seemed less than impressive to me. But since I have been using skin overlays this time, I thought that others might have noticed a difference when using CC as well. I know that CC can mess up a variety of things, so maybe offspring appearance too? *Shrug*