It seems that for some quests Dranei are not being properly flagged as Alliance, meaning that whatever item you are meant to be getting for the quest won't drop. Blizzard are aware of the problem for the Flute of Xavaric quest, but it seems there are others...

Can you recall the exact name of the quest? I could use more accurate search terms to see what's going on with that.

Flute of Xavaric is currently bugged in the manner you describe. Not dropping for Draenei. We're in the process of getting a fix for that particular one.