The "CSS Frameworks" like Bootstrap, Foundation, etc. tend to be very opinionated and therefore, for some aspects, difficult to customize. The production sites on which I've worked generally want to project their own unique identity and not look like the "million other Bootstrap sites on the internet." It often ends up being harder to override the BS/Foundation/etc. styles than simply creating a framework from scratch.

Also, as others have noted, the large frameworks tend to be ... well ... large. That can definitely drag down performance if you're forcing a bunch of CSS into a browser that isn't actually needed by the site.

BS is ridiculously bloated.