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It's not just scanned books. I found a number of minor issues with an ePub file I bought that had been exported from InDesign. However, most of those problems were almost certainly due to markup tweaks that the ebook designer made (a missing letter at the end of a line where a <br /> tag had been added, missing space after a bolded footnote marker, etc).
From what I can tell, it looks like the source materials used for the ebooks are generally pretty clean from a proofing standpoint, but there really doesn't seem to be any rigorous proofing after the ebooks have been created. This is contrary to the method used for print, where the final layout versions get one or more thorough proofing passes (of course this doesn't always catch all the mistakes either). Since a fair amount of stylization tweaking gets done during the layout process (for print) and coding process (for ebooks), the output versions from both processes need to be rigorously looked over, which isn't happening.
Of course, it also doesn't help that many of the publishers are leaving the ebook formatting up to the resellers.
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