There are some use cases for Bootstrap for sure, but I feel you need grasp the basics of CSS first. It is like using jQuery for everything instead learn proper Javascript.
Until you get to the point where you are reinventing jQuery vs just using it. The same thing can happen with CSS, you are formatting all this stuff, getting a layout, spending tons of time fixing layout issues in CSS, etc. Where your time might be better spent just using Bootstrap and working on your app vs CSS.