The phenomenon of stems remaining green while soybeans inside pods are at or below harvest moisture is nothing new. It's been noted for decades. It seems to be worse in stress years, and from reports coming in so far, this year is no exception. If that's the case, the best advice is to check the beans within the pod to determine when grain moisture is ready to harvest. Don't rely on the weather-beaten plants to give you their normal clue.
One farmer reports harvesting late Group II soybeans, more suited to Indianapolis and north, with a yield around 20 bushels per acre. The field was planted in very early April during the warm, dry stretch for planting.

The beans only tested 10% moisture, he notes. That means he lost weight compared to selling them at 13%. Elevators dock for moisture levels above 13%, but they don't pay a premium if soybeans are drier than the required level. The result is less weight to sell because there is less water in the beans, and water has weight.
The problem in judging them was that the stems stayed green, even some of the pods, the farmer says. By the time you figure out that the beans are mature and ready to go, they've already dropped to a lower moisture content.
The other problem with running green stems is harvesting them properly. It can be more difficult to run green material through the combine, namely the stems, and get the same quality of threshing and cleaning as when the stems are mature and brown. This may depend partially upon what model of combine you are using, and what threshing method your combine uses.
The best advice, however, is to check fields closely. Don't wait for all the leaves to fall and certainly not all stems to turn brown before checking grain moisture of the bean inside the pods.