I'm running Nui+ version 5. I have really basic addons running with it:
1) The tooltips for loot dropped (when you mouseover an item to see if you want to roll on it) flickers so you can't really see it. Not such a big deal, but annoying.
2) Today I was raiding in Firelands and everything was going fine with Nui until I hit this giant Bird Boss. (Alysrazor). These empty feather icons appeared over my buttons. Which wouldn't be a huge deal except it kept me from casting anything unless I opened up my spellbook. So strange I know. I wish I took a screen shot.
I disabled nui and everything worked fine on our 2nd attempt. (I managed to wipe the raid on the first).
Anyway--I'm a level 85 Shadow priest. Dont' know if that helps or if you need any other info. I couldn't find any other bugs like this in the forums.