Hi, 

It could be any number of end of the growing season factors. You can explore our web resource about growing beans and the possible ailments. This time of year with the nights cooling and recent wet weather, it could be attributed to anthracnose which is a common disease in cool wet weather. You can refer to the Virginia Tech article for more information on it. It is difficult to see in the photos if this is what is forming on the beans but you can follow the guidance for clean up to help prevent it in the future.

It is fine to harvest what you can for the beans and they should be fine to eat as long as the pods are not rotting and are solid. You can just be sure to inspect the bean pods and any that look too damaged or not edible, discard in the compost. You can also take the beans out of the pods and eat those - they should be fine. 

Let us know if you have further questions. 

Emily