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You could have a smaller invader in your coop. A mouse or rat perhaps. Maybe set up a camera and see if you can catch the culprit in the act.

No way a crow or raven could fit through that opening. They're practically chicken sized. It's probably your chickens eating their own eggs. If an egg accidently breaks, they'll quickly devour contents. They may have played keep away which is how some of the eggs ended up in the run.