After completing 'Heart of the Alliance', Alliance players while be phased when visiting Shrine of the Two Moons, in what seems to be the phase for the quest that mirrors Alliance side.
Approaching the shrine but still in Valley of Eternal Blossoms, you can see any horde players that are outside the shrine and still in sight range. Once you switch to the subzone 'Shrine of Two Moons', it phases. All horde players are no where to be found and there are Sha-Touched Grunts littering the terrace.
Relogging and the usual attempts to fix the bug have failed. I have progressed further into the quest chain to complete 'Secrets of the Past', but I am still phased.
This bug makes it impossible to PvP at the shrine.