From what I recall of
Cory's website, the deal is that he puts up a single format of each book he releases to creative commons (I don't remember which format, but it's not ePub), and then encourages people to convert them to other formats and he puts up the first contribution for each format on his website. Furthermore, these versions are missing the covers because his publisher paid for the cover art, and these are not the publisher editions, so unless the artist has also contributed their cover to creative commons, Cory doesn't have the rights to include the cover.
Unfortunately, this means that some of the editions on his website are actually poorly formatted, and won't ever get replaced by better versions. So, if you don't like the version you downloaded, feel free to grab the original format and convert it and clean it up for yourself, buy the publisher edition, or suffer the poor formatting.