It kind of boggles my mind that there are Draenei out there going through the Onyxia quest (not just because they're not supposed to be that level yet, but also because who still cares about Ony?), but apparently there are, and they're having issues. It seems the Draenei aren't yet considered to be in the Alliance for a few quests-- the note in A Crumpled Up Note isn't dropping for them at all. Also, the Flute of Xavaric, another Alliance item isn't appearing for them either. Drysc confirms it's a bug, and they're working on it.
Which is a little strange, when you think about the mechanics of the game. One player mentions the Horde's experience with the necklace in Uldaman-- when Horde try to pick up that necklace, they get an error message (but at least it drops for them). Likewise, Blizzard was able to easily make Pally gear drop on all those Horde runs before the expansion, but they can't flag the Draenei as Alliance? Bit of an oversight, that.
But here's hoping it'll be fixed soon, and the Draenei can be folded back under the wing of the Alliance forces for good.