The most common cause of brown spots on beans is from a fungal disease called anthracnose. It's caused by a fungus that's fairly common east of the Rockies and thrives during periods of warm, moist weather.
To combat, remove and destroy any diseased plants. The disease spreads rapidly on moist foliage so do not work in your bean garden when the foliage is wet. Do not plant beans in the infected area for two to three years and try to buy new seed that's been grown and packaged in the western states. Rotate your beans every year."