Here are a few things I dislike about Bootstrap framework :
In my opinion Bootstrap is not semantic and the presentation is not separate from content. This makes scalability and maintenance more challenging.
I use a framework to get started quickly. But in case of Bootstrap most of the times I end up overriding a lot of CSS rules to suit my needs. It would have been great if Bootstrap offered just the bare minimum CSS. Of course this is great for prototypes, but not very good for serious website development.
The SaSS support just came recently with Bootstrap 4. The previous versions should have been on SaSS, IMO.
You can say Bootstrap is a bit bloated if you consider the lines of code and file size. Apart from the file size the DOM produced by Bootstrap is also heavy. To fit your elements in simple grids you need to add a lot of markup, rows, columns etc.
No easy upgrade. I can't upgrade one of my Bootstrap 2 projects to newer versions because of lack of backward compatibility.
P.S. I still use Bootstrap for prototypes. For serious production apps I prefer vanilla CSS.