I tried it last year on very young plants that I was "holding" in a container until the container I was to plant them in was ready. I had a few other plants the it wasn't used on that were in a different container. What I found is that it initially gave the starts a larger root system than those with out it. I didn't end up growing the ones that didn't have it, so I don't know if that would have mattered over the course of the season. I didn't notice much different between the plants because it was only for a few weeks. I fully expect that any continued benefit would be lost because the container temp would kill the myco as the season progressed. As I understand it, that is part of the problem with using anything like this in a container; ground temp and the temps in a container are very different. High and low temps temporarily kill/stop organics from working, so you can't count on them working.

Innoculation introduces beneficial bacteria to the seedling's roots so it has an easier time fixing nitrogen. Plants that aren't innoculated might not be as vigorous without fertilizer. But if you're lucky, the beneficial bacteria might already be present in your soil, especially if you've grown beans in the area before. You don't have to worry too much. They might benefit from a bit of fertilizer if you think they need it.

Xerophyte is right. Spots like you describe often mean terminal illness. If the rot started in the roots, or at ground level, it could be slowly hollowing out the interior of the plant. It may already be too late. Remove it from the container and examine the plant carefully. It is possible that surgery can save it, but that only works if the rot is external. Rot moving upwards in the vascular tissue can only be salvaged by transecting the plant above the level of the rot.

Whether to us it or not is a matter of choice. I use it when planting in areas that didn't have legumes in them the previous year. Innoculant gives you healthier plants and higher yields so that's why you would use it. It improves the plants performance in the currant year not just improving the soil for future years. When you grow in containers using slow-release organic fertilizers, the beans need all the help they can get because beans produce relatively quickly, meaning they are needing to grow fast and produce fast but they are in an organic mix that generally is taken up and used more slowly. By innoculating the bean seeds at planting time, you're enhancing their ability to fix nitrogen from the air which allows them to capture nitrogen from the air continuously to supplement whatever nitrogen is in the growing mix. Remember that every time it rains or every time you water, some of the nutrients leach from the container, so beans that can fix their own nitrogen from the air are less likely to stall or slow down because they are short on nitrogen. After I plant my beans in the ground, they never get fed again by me because they can get all the nutrients they need from the soil or by fixing nitrogen from the air. When you plant them in the containers, it is a little more complicated than that since you have no way of knowing if there are any beneficial microbes or bacteria in your potting mix that will help them. (Unless you've added those too.) I think it likely that bean plants need the innoculant more in containers than if they were in the ground. Will the beans grow and produce in containers if not innoculated? Sure. But I believe they grow and produce better with it. However, you'll never really know for sure unless you plant identical beans in identical pots, using innoclant with one and not with the other to see if there's a discernable difference. Dawn