I just ran into this on my hunter. The same thing was happening on a WQ for my druid in the area a few days ago ( World Quest Scrolls &Scales.)
I started thinking it might be related to having the quest involving the Xal’atath blade & the altar in this area, so I completed the 1st step of the quest, but the area didn’t revert phases. I left the area, came back, but as soon as I enter the area the quest objectives/mobs phase away & change from Dreadcoil naga to Darktide. I tried logging out/in, same.
I will complete the entire quest chain for Xal’ataths blade & come back to see if it’s the quest chain bugging the phasing or something that came about from recent patches.