Thanks for the replies!
I will check at night, and we do have little furry critters running around.
The thing that really gets me is that the seeds had little holes in them too, which I can't imagine a mouse/chipmonk/squirrel being able to do, but I've been surprised by the little buggers in...
So, I'm hoping someone can confirm or deny a theory for me. I have a few species of cayenne in one of my raised beds and fruit are just starting to ripen. On one - just one - of the plants, the first 4 fruits have developed big holes in them with dark edges. I pulled a few and snapped pictures...