If I had to guess, I'd say slugs. They did a number on my peppers last year when we had an unusually wet summer (I found some IN peppers that I had picked. I didn't always notice the small holes. Even hot peppers). I've seen them on my rhubarb too.

Beer traps work to an extent. I don't know for certain, but I believe that sluggo is approved for organic gardening. Diatomaceous earth is organic as well.

Hope that helps -- good luck!