Undercooked beans, while not parasites, can make a person very ill, especially if they're kidney beans. How fortunate that you only undercooked pintos. Soaking helps. In fact, unless you have a pressure cooker/canner, I would always soak dried beans for at least 12 hours before cooking them. Freezing, as someone else mentioned, also helps in killing any "bug" that might be present in dried grains and legumes.
In general, cooking is a great thing. It banishes all types of ills. I've never confused an undercooked bean with any of the specimens you presented.