I can relate to this personally. Until I started college, I really understood what I was learning. I enjoyed doing science and reading about. But then I made the biggest mistake of my life - I didn't put enough effort into preparing for the IIT entrance examinations and didn't make it in.
I started at the second-tier college that I went to and I realized that my teachers didn't know what they were teaching. We were supposed to be learning all this stuff about Fourier series and Laplace transforms, and I couldn't figure out where we were going with all this. I couldn't understand why certain assumptions were made and where they mattered in the proofs. It was all going above my head. When I asked my lecturers, I was branded as a disruptive student. I simply got insulted until I learned to keep my mouth shut.
I didn't do very well in my examinations either. The most marks were given to the students who could reproduce what the teacher said in the cleanest handwriting with the best figures. My writing sucked and my figures were dirty, and I wrote what I understood not what I remembered. I simply had no hope.
A few years later I started a master's degree at a top-tier institution. Man, was this a different experience! I realized I could ask questions and get intelligent answers. I realized my professors actually knew what these proofs were going to useful for! I was finally back in an environment where understanding was valued.
Unfortunately, I still haven't recovered fully. I can see myself understanding more stuff than in the past, but it's something I have to force myself to do. I use tricks I learned from Feynman and others - I try to build a visual model in my head as I'm hearing something and then I ask questions to the model to see if I'm really understanding stuff. I force myself to think about stuff all time. But this process is not automatic, and I can't help but think my undergraduate lecturers beat it out of me.