Comment by Finnucane

I oversee ebook production for a university press publisher, and indeed, our typesetters have to do some pre-processing of our authors' Word files before typesetting (we do all editing and copyediting in Word), and then post-processing of the Indesign output to get acceptable ebook files. There are some plugins that will help. Indesign, left to its own devices, will give you garbage.

Our sales vendors all check the files with epubcheck. If it doesn't pass, they'll bounce it.