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Possibly thinner shell, the bumps on the outside could also make it easier for the pigment to pass through, or it just spent longer inside the hen getting painted. I've noticed it most on eggs that have speckles.

Yep it's just the color from the shell going through. It's perfectly fine to eat. I've seen it lots of times even in store bought eggs.

Are they brown eggs? If they are it's far more likely it is the brown pigment leaching to the inside of the shell through the pores.