Board Thread:Questions and Answers/@comment-28116944-20170110175534/@comment-24577221-20170110203742

Rare eggs look exactly the same as their common counterparts. It shouldn't be possible to have two eggs in the same structure at the same time; if you have, it's a bug / glitch.

I assume that you're not talking about the two egg-like things at the top of the breeder while it's running, of course; those represent the "parent" monsters.