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I was having the same problem with some of my epubs. I was getting errors stating that there was an error with an opening and ending tag mismatch. I was able to fix my problem in calibre by right clicking the problem book and selecting "edit book". Inside the editor, click on Tools at the top, then Fix HTML - all files.
The only code that was removed from each file was this:
<meta content="http://www.w3.org/1999/xhtml; charset=utf-8" http-equiv="Content-Type"/>
and an extra line break after the closing </html> tag.
This has fixed the problem I was having.
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