Whomever ended up with my old copy of The Caine Mutiny will find a lot of stuff written in the margins of the first few chapters. That’s as far as I got in reading it, and I riffed it quite a bit. This was in 6th grade (and yeah, maybe the book was too advanced for me at the time), years before I had ever heard of or seen MST3K.
I have a copy of Who Built the Moon? which is annotated by someone who read it critically and calls out poor (or lack of) scientific thinking. It’s wonderful.
I just remembered- my father published an annotated version of The Time Machine and somewhere I have the book where he cut out every page of two identical paperbacks to paste each page side individually into a larger blank book and wrote all of his notes in the new margins. I’ve never actually looked at it though. His handwriting is pretty hard to read.