The realms are down this morning for "scheduled maintenance," and in the meantime, here's a list of what's wrong (and hopefully what's being fixed right now). Blizz QA guy Hortus has posted a list of known issues in 2.1, and I've included it in full after the break.
Most of these are pretty inconsequential and/or already known, but a few of them might cause confusion (I had the "grayed out" icon thing happen to me just last night-- the spell looked like it was unavailable, but I could still use it). They all seem easy enough to fix, and so hopefully when the realms go back up today, we won't see them again.
Strangely enough, there's no mention of the Hunter bug/feature at all, so Blizzard still hasn't confirmed that one officially (or maybe hunters liked using it so much they just didn't want to report it). And though Neth has confirmed the Spellthread nerf as a bug, it's not on this list either. I guess we'll have to see what drops this morning-- we could get a small post-2.1 patch, or maybe we'll have to wait for further hotfixes to see any of these bugs squashed.