This quest is so horribly bugged i cant even stand it. I cant even really see the npc's needed cause the terrace is flooded with giant Sha incarnations. If i decide to knuckle under and try the quest anyway some of the Kor Kron elite turn into Sha but stay friendly and i cant attack them with anything but AoE and as a Rogue i dont really have good AoE. And before the answeres of abandon quest and re accept or fly out of phase and come back, i have done all that and still have these issues.
Never noticed anything problematic when I did it. Dunno what to tell you, if reloading and such doesn't fix it. You don't need to kill that many, so if you're able to get any credit for the kills at all, stick it out and it'll be over and done with before long.
You can try putting in a ticket for it, Blizz might be able to sort it out later and spare other people the grief.