well, what is undoubtedly related to the new update... The Stonecore on Normal and Heroic has no mobs, npcs or even critters spawned inside it, completely clean... probably has to get mobs phased in or spawned or something
probably related to the quest 'Wayward Child'
edit: way way bigger problem... once you finish all deepholm quests and take portal to Stormwind (assume Orgrimmar is the same) there are no NPCs, no portals.. nothing... abandoning quest and relogging fixed it, will see which part actually did fix it in some time
edit2: way way way way bigger problem... you need to relog once leaving deepholm for 'the normal world' to load up, a reload doesn't fix it