Most often holes in the leaves of bean plants are caused by the Mexican Bean Beetle, the black sheep of the Lady Beetle family. These wee thingys look similar to all the other Lady Beetles except they are yellow. If you have them the first line of defense is a trap crop of soybeans or floating row covers, or both. There are several predators (spined soldier bugs, parasitic wasps) that can be encouraged to hang around by interplanting flowers and herbs (often considered "weeds") that attract these buggers. Late types of defense would be Neem Oil Products or pyrethrin products,
For the future look closely at your soil and work at making that soil into a good, healthy soil, because plants growing in good, healthy soils that are strong and healthy are better able to withstand insect pests and are most often less desireable to them.

You might also consider earwigs. They have been my problem this year. I have a picture of what they have been doing to my plants on my blog.

Here is a link that might be useful: My SFG Blog

If they look like they've been shot with a tiny shotgun, suspect flea beetles.