Teleported from Old Dalaran (at rest) to Orgrimarr with the Mage spell. Loaded into Org having been randomly flagged and unflagged for PVP. (5 min wait).
This is still happening in both Stormwind and Dalaran (Legion) as well… 
For Stormwind (Legion), I simply finished the first big cutscene for Legion (after Battle for the Broken Shore quest) and flew on the provided griffin complete the quest. When attempting to pick-up the quest “Demons Among Us” an opposite faction player showed-up and killed everyone in the throne room, including myself. Unsure how I was auto-flagged.
For Dalaran (Legion), I was mounted on a party member’s Sandstone Drake and we entered the Chamber of the Guardian teleporter for the quest “A Falling Star.” I was auto-flagged for PvP, but my party member was not. Unsure how I was auto-flagged.
I suspect the issue in Dalaran has to do with improper vertical mapping of the PvP area in the Underbelly, so sometimes flying along the street you can become flagged. I also recall an autoflagging issue I ran into several times (not lately, as I haven’t played a warlock there for a while) at the entrance to the warlock class hall.
Not sure whether it’s possible to have a pvp combat in sanctuary even flagged.
About Stormwind , Orgrimmar and Oribos, these areas are shared between warmode and nonwarmode phases of the realm. (let’s say whenever you toggle warmode you are phased). That’s why whenever you turn warmode off in these areas it still leaves you flagged for 5 minutes, as well as entering and leaving bgs.