I have never seen anything like that. I’m sure you know they just have nubs for thumbs. Is it possible that he is chewing the nubs like an obsessive compulsive disorder? If he is chewing them it’s probably infection with a possible abscess. It can’t imagine that it would be poop. His entire paw would be caked if that was the issue. I’m sure his cage isn’t that dirty that it could be poop.
Rats get a condition called bumblefoot but it’s on the bottom of the feet. It’s basically ulcerations from walking in a dirty cage OR a wire bottom cage. It’s an infection. I have never seen it in squirrels but I suppose they could get it.
https://www.thesprucepets.com/bumble...n-rats-1238512
You say you were out of town camping. Did the cage get dirty while you were gone?
I still think a soiled cage would cause issues on the bottom of the feet, not on the thumb nubs.
Do you have a vet? Can you give us an idea of where in FL you are as we might be able to recommend a safe vet.