Yup, those are bug bites. Something takes a bite out of them when smaller, and the wounds callous over with brown tissue in an attempt to heal the wound. The hole enlarges a bit as the bean grows, in the way that something written in magic marker on an uninflated latex balloon gets larger when the balloon is inflated.

Now, exactly who the culprit is I can't say, but I've seen this happen enough times in my own garden to tell you there are multiple possibilities -- earwigs, grasshoppers, various beetles, even slugs during wet weather (especially on bush beans).

Pretty common to get spots on bush beans in hot August in the midwest US for various reasons. Insects mostly, slugs, fungus... Cut off the bad parts if you can, eat the good parts. You could try poison powder in June and July to try to keep them pest free, but I don't want to fill my garden with poison. In Ohio I usually mostly give up on them in August since the beans get less appetizing.

I don't know an easy solution, but avoiding crowding may help.