There was a glitch a while back.. You could be flagged by someone from the other faction if they attacked a mob or the same group of mobs that you were already attacking.. This was an old glitch and I thought it was fixed a long time ago..
The other issue that confuses me is that I was unaware you could ask players of the opposing faction to duel?? I will have to try this and see.. I know it didn't work in the beta.. I would think you wouldn't earn any valor from a duel with someone of the opposing faction..
Something else that has been happening, at least until recent patch, AOE skills that companions or players use can also hit someone from the opposing faction and hence flag the player for PVP.. Again, I heard that this was fixed as well..
Beyond that?? I saw a lvl 19 on Ilum tonight, so that stuff still isn't fixed.. So who knows what is or isn't fixed anymore..