ok last bump, since I figured out what happened and how to avoid it in the future.
Basically at the end of a mega war (claim on iron throne) I was allowed to imprison a bunch of people (jaime and cercei's kids). Seeing how they all had claims I thought to myself why not execute these prisoners.
Once they were imprisoned their liege changed to some foreign person, in Pentos or somewhere else out there, and when using the execute button all it said was that the lords of Pentos (or wherever) would not be happy and I'd get a -10 penalty to opinion. Nothing about tyranny so I gladly executed them.
The thing is that executing did indeed give me the vanilla tyrant penalty to some lords (as mentioned above with the high septon) but it did not give me the GOT mod tyrant trait as you usually get when being a tyrant. So doing it that way, when I'd go to legally imprison characters, and I'd imagine other tyrant free legal actions, I would get penalized by the on action event: adding the correct tyrant trait (-5 to -15 etc) and removing my character's just trait if they had it, because some lord had the vanilla tyrant opinion modifier on me... or at least that's how I'm reading the event scripts. Might be off I know though it seems to be making the most sense. These being the on_actions 150 through 154 if I remember right.
I suppose if those imprisoned changed their liege lord to someone within my realm it would of prevented this, or if the illegal executions did add the tyrant trait as I guess it should have even with those executed being in another realm, would've fixed the whole problem.
At least now I know to hold back on killing people in my jail if it says penalty to opinion even if it doesn't mention tyranny. Or any other action with the same explanations, and I've as yet encountered weird unjust actions.