I noticed, that in some ebooks the internal links do not work and only some (not all) chapters are displayed in the ToC. Unpacking the epub and changing it's internal HTML structure revealed that the problem is in files containing spaces or characters like [ ], which are escaped with sequences like %20 internally. Removing such chars from all the filenames at least made the links work.
you can see an example here:
http://cthulhuchick.com/free-complete-lovecraft-ebook-nook-kindle/
in this case, only the space-less chapters are shown in the ToC. In the case of my ebook (about which I do not know whenever I might redistribute it), the ToC is not displayed at all, despite the ePub having a toc.ncx. I _think_ it might have to do something with the book's title being not entirely ASCII.
Can verify the issue to happen on both Android and Windows
This patch fix bug.
But if epub contain files with Cyrillic name, this is not work (may be bed unzip encoder)
epub with cyrillic files. Contain 4 chapters.