Playing boomkin druid, starsurge missing from spellbook, seems most classes are missing the spell given by spec.
IF your tracking a reputaion, you get a lua error everytime mouse goes over the rep bar.
Ink trader in Dal, now trades the new Jadefire? for your older ones, so you can’t purchase any inks from him.
Can’t leave dungeons as well.
Couple of these are addressed in known issues, and there is a work around for the leave dungeon issue until its fixed if you want it 
The ink trader change isn’t a bug, it’s what they did during the original cata launch.
Specialization spells (ones given by the spec instead of through talents) seem to disappear when you log off. You can get them back if you have dual spec by swapping to your second spec and then swapping back to the spec you want to play. I would guess that paying for a respec would also work, but I haven’t tested it.
I feel sorry for the devs who have been working overtime trying to polish this release and will be forced to work even more overtime to fix all of these bugs that they couldn’t address before they were forced to launch the prepatch. Old Blizzard would have delayed the patch if they knew it was going to be this bad.
Logging out and back in makes the titular spell of my class disappear. For example.
Affliction warlock: No unstable Affliction
Resto Shaman: No Earth Shield
Furry Warrior: No Dual Wield.
ect ect. Currently the only fix for me is to have dual spec and to swap between specs to get it working again.