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Actually, I wouldn't be surprised if it were book related. Maybe it lays in the way the tags/lines indications/whateverThisIsButICantfindTheRightWord were written.
As regard for the footnotes, on one of my books they were at the end of each chapter and on the one I'm currently reading I guess they are at the end of the book. So the actual location doesn't seem very relevant.
Is this a sideloaded book? If so has it been converted to Kepub?
If the issue is because of a bad tagging maybe you can try to convert it epub->epub or epub->kepub with Calibre.
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