What's the most likely culprit?

[Mahlzeit]

We put inches of filter sand over our hardware cloth wire and feet don't touch it. Any vole traces in the area?

You lost me on this one how do you keep sand from falling through hardware cloth? My coop is elevated it's not sitting on the ground

 

[Mahlzeit]

I put some fencing that I had around the bottom and whatever it was came back and dug at it a little.

 

[MeeMa Brown]

You lost me on this one how do you keep sand from falling through hardware cloth? My coop is elevated it's not sitting on the ground

sorry, our coop is elevated but the run is under it and 8 ft beyond so, the floor is 4x12 ft box made of 4x4 lumber so we stapled hardware cloth on the bottom. Buried it the 4in.
And filled it with course sand. Coop-run walls placed on this foundation.

 

[John Roth]

Coon or mink. And both are very deadly. I suggest putting out live cage traps.

 

[Mahlzeit]

sorry, our coop is elevated but the run is under it and 8 ft beyond so, the floor is 4x12 ft box made of 4x4 lumber so we stapled hardware cloth on the bottom. Buried it the 4in.
And filled it with course sand. Coop-run walls placed on this foundation.

Ahh I understand now