This looks like it may be a disease called pod and stem blight caused by Diaporthe sp. The black dots you are seeing on the pods are likely fungal structures called pycnidia - these house the spores of the fungus. Usually these symptoms occur later in the season as the plant matures (why you are seeing them on the aborted pods instead of the green pods on the same stem). You will see lines of pycynidia running down the stem and petioles. This is pretty distinct to this disease so keep an eye out for that. This disease can also be confused with anthracnose which also produces black structures on the stems and pods, but usually they are a little more blotchy than what is shown here. This disease can be seed-borne and reduce seed viability and seed quality so make sure to check your seed if you plan to replant next season. #podandstemblight

It seems it is the same as the Bean Bruchid Beetle Insect https://en.wikipedia.org/wiki/Callosobruchus_chinensis The Jimma soybean program has been working on common bean too, and this insect has been a problem on common bean alone, and now it expanded its host range and started attacking soybean. This is just a recent phenomenon. #bruchid

Amado was correct - you have a disease that is commonly referred to as white mold or Sclerotinia stem rot which is caused by Sclerotinia sclerotiorum. You can see the actual fungus on the stem - the white mycelia and the black, round sclerotia sitting on top of the mycelia - as well as the bleaching and rotting of the stem that is caused by the fungus. It is a fairly common disease and often occurs wherever soybeans are grown in cooler and wetter environments. It is also a problem on beans and sunflowers, but not maize. Often times crop rotation does not effectively work because of the broad host range of the fungus and the long lasting survival of the sclerotia. Using Trichoderma could help in reducing the disease but may not eliminate it. I would discard those soybean plants that have symptoms (rogue them out before harvest) and then I would carefully sort out the seeds from the remaining plots discarding any debris and any discolored seeds. The fungus can be transmitted via seed or debris in seed lots. #whitemold #Sclerotiniastemrot