The sections in the preface (from "To Everyone" to "References") are all listed in the TOC, but they are all linked to the same page (the first page of the preface).
The "References" and "Homework" sections in each chapter are linked to the "Summary" sections.
The final "General Index", "Asides", "Tips", and "Cruces" are listed under "Persistence". They should be standalone instead.
These are not big problems though. It seems that they are caused by the LaTeX format used. I'm not sure if they are easy to fix. (Maybe just modify the PDF output if it's hard to fix in LaTeX?)
The PDF downloaded from https://pages.cs.wisc.edu/~remzi/OSTEP/book-electronic.html has several incorrect TOC hyperlinks or structures:
These are not big problems though. It seems that they are caused by the LaTeX format used. I'm not sure if they are easy to fix. (Maybe just modify the PDF output if it's hard to fix in LaTeX?)