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Hard to say without seeing the epub but possibly a problem with the Table of Contents file (the .ncx file, not a page in the book with a list of hyperlinks). You could try using the calibre main Editor or TOC Editor to see if you can see any anomalies such as
- sequence of TOC entries is different to reading sequence contained in the .opf file <spine> section.
- some content files don't have an entry. Although this is mainly a problem with kepubs rather than plain epubs.
- presence of a problematic page-map file inside the epub
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