From Yechalew Sileshi (EIAR, Jimma, Ethiopia)
What is this disease on my soybean plant?
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.