What's the weather been like? I notice that happens when it gets hot. Maybe the beans are trying to mature a few seeds before they get killed by unfavorable temperatures.

I agree with fliptx. Dale

I am surprised that you have so many disease problems... do you get the coastal fogs that far inland? Unless I am mistaken, you are in the foothills. When I lived in San Diego, the coastal fogs generally disappeared around July. Fog, or excessive overhead irrigation (or rain?), are the most likely causes of the bean diseases.

Heat can cause the problem you describe, although if you have had fog, it may not be the culprit. Not keeping plants picked can also cause thin tops... and sometimes, a heavy crop is followed by deformed pods for a time.

I would recommend removing all pods; the plants should respond by resprouting & developing new blossoms. Some varieties "rebound" better than others. I would also recommend mulching around the plants, if you have not already done so. Mulch will allow you to cut back on the watering, which may reduce some of your disease problems; it will also keep the roots cooler in the summer heat.

The reason for wide bottoms is poor pollination. if you cut open the bean there will be no seed in the top and only one or two futher down instead of a full pod. Beans pollinate the night before the bloom opens. same as tomatoes. If the humidity is to high the pollen clumps and does not set fruit this also happens to the tomato. I have also seen this happen on older plants which is probable not due to weather. I'd say it is time to compost those plants and plant now for the fall.