I have made my first website using MVC 5 which works fine on my local machine but when I publish it to the server some of the CSS is not minifying correctly.
My solution was the same as @GraehamF, I was having issues where the @imports were trying to load the css, when you inspect with dev tools the bundle css's if you see something like "run-time error", it means the file is not loaded correctly.
Before to deploy remove the debug="true" on your web.config then try to run the code on your local box, that should give you the idea of which files are not getting loaded and causing the bundle did not work.