Yes beans that are soaked too long can go bad.
When the beans are soaked in the water too long such as in over 24 hours then the beans can begin to sour and then go bad and need to be thrown out.
The longest you really should need to soak beans is 10 to 24 hours before cooking them and any longer than 24 hours of the beans soaking then they will begin to go bad.
I soak beans overnight and then drain the water the next day and then put fresh water in the pot and then cook the beans.
Or most times I will put the beans in the slow cooker after soaking them overnight and allow them to cook while I'm away from home.