https://github.com/twbs/bootlint
I could see myself integrating something like this into a text editor or a build process -- something that watches for bootstrap usage errors and helps my team correct them early and quickly. That is, of course, assuming that we stick pretty closely to vanilla bootstrap, which we usually don't.
One of my biggest issues with Bootstrap (and similar frameworks) is that, beyond a certain point, you find yourself overriding and customizing them to such a degree that it's more productive to just build your own "vanilla" components that are specific to the way your site or organization uses them, and then just ditch Bootstrap altogether.
One thing I'd like to see is a way of generally linting HTML structure (not validity, but actual structure) with a goal of reducing complexity and improving maintainability, regardless of what frameworks you may be using. Something that spits out a ratio of meaningful, semantic markup to "div soup" and tells you where you should spend the most time mopping up the soup. It could also have some understanding of which kinds of div patterns are acceptable -- bootstrap components, your own component library (see: OOCSS), etc.