Many of the spots are actually just soil on the leaves, or places where the dirt sat too long, and killed a small portion of leaf. The soil is probably from splashing off the ground during rain. The soil dissipates throughout a droplet, then settles in a layer where the droplet was after drying off. The dirt should come off easily with a light rinse with ambient purified water. Also, cleaning the leaf undersides usually has more effect toward increasing plant health, because lots more dirt gets splashed on there.
Real bean rust is easy to see, as it invariably develops a yellow patch around each infection. Here are some photos to compare against:


Your plants actually look fairly healthy, and if you keep a good eye on them and catch disease early, you should get a good crop.