Originally Posted by ATimson
Well... the books are probably converted from the laid-out-in-InDesign version, rather than the manuscript version (otherwise they'd be missing any revisions made from the page proofs, etc.).
If they're not doing the layout in InDesign "right", so that its ePub export knows how to handle the line-break/hyphenation issues that crop up in a PDF, I'd expect to see similar errors. (And the resulting PDF ebook probably fails at reflowing properly on mobile devices, too.)
Vince Flynn's books do seem to have a particularly horrible problem. I bought one not so long ago for my Kindle, and it was missing all the quotation marks, dashes, and full stops. I kept it, because it was a good story, but the almost complete lack of punctuation made it a "challenge" to read, especially the dialogue parts of it.