Here's an example of a location where the inhabitants are supposed to all be the same faction, but kill one another as soon as you enter the cell.
Upon entering Odirniran [CELL:014802C8] (as a member of House Hlaalu for the Telvanni at Odirniran quest), Haleneri Salor [ACHR:01813E5C/NPC_:0126016F] and Valyne Vedaren [ACHR:01813E5B/NPC_:0126016E] immediately attack Remasa Othril [ACHR:01813E5A/NPC_:0126016C].
I used the "stopcombat" command on all 3, but then they immediately turned to attack me (I'm supposed to talk to Remasa Othril for the quest). I used "stop combat" and "moddisposition 14 100" to make them stop attacking me, and then they went back to attacking one another (eye-roll emoji). I finally resorted to a script to stop all the shenanigans (see below).