Feel like it’s impossible that you haven’t heard about this yet, since it’s been going on since prepatch. Maybe you could fix it by just setting factions that start as neutral to actually BE neutral when loading in.
Killed by Defenders of Malorne after zoning out of the Molten Front back to the Regrowth. Were hostile when I came out, stayed hostile until they killed me, back to friendly when I rezzed.
This has happened to me with: Steamwheedle factions, Argent Dawn, Hyjal factions, Cenarion factions, and Earthen Ring factions. To reproduce just take the portal from anywhere to a place guarded by one of these factions, and 9 times out of 10 you will see it happen.