What predator could have done this?

[Strikefalcon]

I agree with Kev. I have 2' chicken wire folded and sticking out a foot at the base and covered with dirt around the perimeter of our run

 

[tellynpeep]

Chipmunks, squirrels, or rats is my guess. Whoever it is is building a nice nest in your nestbox! A friend of mine saw a chipmunk carrying intact eggs our of her coop...

 

[Chookpensbuild]

Set the trap on this place