I think that one of the main reason why they have such problems is because they treat the TOC like any other content in the book.
When you create an e-book, you shouldn't have to manually create the TOC yourself. On Feedbooks, the TOC is created automatically (PDF/epub/Mobipocket) using the semantics of the book. A system that treat a book like a huge chunk of text/HTML, without any sort of mark-up dividing the book into multiple elements will always have this sort of problem.
This is a huge problem. It means that if one day, Amazon switch to another format, let's say epub, they'll have to ask every publisher to re-upload their books.
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