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Most likely your source format has apostrophe's escaped to entities using a bad syntax. Did you confirm that they look correct in the source document with a native viewer for that format? If your source document is correct then you should open a bug at bugs.calibre-ebook.com
As Manichean notes, if the problem is your source format Sigil is the best bet to fix it, after you do the conversion from mobi to epub.
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