Pretty much the same thing happened to me on a late-2013 MacBook Air. Installed Yosemite as an App download over Mavericks. Everything else seems to be fine although I haven't tried my external drive with the TM backup -- probably won't until I know it won't be screwed up.
Haven't previously used FileVault in 6+ years of owning Macs but naively agreed to use it during the Yosemite set-up. Big mistake. From what I can tell, my "fatal" error was not leaving the MacBook plugged in while FileVault ran through its initial encryption routine. Apparently, there's no easy way to fix this mistake or reverse the process & opt out of FileVault but then, on the other hand, a big kick in the kiester to Apple for NOT warning people during setup that (1) encryption takes X amount of time, and that (2) the power cord needs to be plugged in for that whole time. Did, however, say NO to FileVault when doing a Yosemite install + set-up on my late-2013 iMac. All is well there.
I've been on Chat with Applecare today and they couldn't resolve it immediately. They've escalated it to engineers and upper level techs & I am to get at least an update tomorrow via phone call. Will post back to relate what happens and if a solution is provided.
Thanks to all who've posted solutions here - it may be I'll have to use one or more of them!
ETA: the link to bug reports wouldn't recognize my Apple ID either -- maybe this is only for developers or beta-users? Submitted a comment to feedback as well as my Applecare request, so hopefully there will be some action on this bug.