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Hyphens in the middle of words exist within the body text, and are kept across different formats,
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If your book came from an OCR process, it is very possible to have real hyphens scattered through the book, where the print copy had them. Some OCR is smart enough to remove them from the ends of lines, but not all, especially older ones.
If that is your case, you could remove them with search and replace, but like theducks said, what do you do where they are valid, like "forty-two"? If you just have a bad book to start with, your only option is to proofread it and manually remove the bad ones. Very tedious indeed.
One thing you might try--examine them closely in the editor. I've seen the odd book where the end-of-line hyphens came through as "- " (hyphen space), but the valid ones had no space, and I could clean it up by searching out the "- " instances. But never perfect: proofing still needed.