CSS frameworks are like box mix brownies. They're great if you're not picky and just want something fast. 30 minutes and a scoop of ice cream and everything's great.
As soon as the requirements change, you find yourself needing a new box mix, or a new framework.
Dave has a nut allergy, Sam's gluten free, and the only gluten free box of brownies has walnuts? Now what do you do?
CSS frameworks are the same way. Most are designed to be used quickly to generate very similar looking websites with ease. Because of this they don't address certain categories of issues.
Also, they're a type of tool, and are therefore also susceptible to the law of the hammer. There are many developers who haven't learned CSS but know how to apply some classes from Bootstrap and think they can take on large clients. This is akin to making box mix brownies at a dinner party with friends and thinking you're ready to work as a pastry chef in a bakery.
When the client wants something custom, and the client is interested in consistent branding, box mix CSS frameworks simply aren't going to satisfy them. Even if you configure the colors and the gutters and the font sizing, your bootstrap site is going to look just like every other bootstrap site out there.
That doesn't mean that CSS frameworks are always the wrong choice. The mom & pop deli down the street won't need—and can't afford—to have custom branding; they just want to post their menu online so that people can call in orders easier so they can get a little more business.
If you want to get to the point where you can handle larger businesses with their more refined appetites, learn CSS in depth. Learn how the cascade works, and what specificity is. Learn how the frameworks work, and make something from scratch.
And when you're all done, be sure to share what you've made, because brownies are delicious.