SPOILERS warning.
To the glitch:
I have gone completly rebel having planned it the entire game, maybe one shaper type answer at the very first town of South End.
I have gotten to the end of the game, to the Geneforge zone itself. When I enter the zone, I talk to Litalia and she acts like I am a loyalist, and in fact, my responses are of a loyalist. (I will kill you for being a traitor, etc)
Then I ended the conversation without fighting by clicking the check button. An auto-dialog immediatly poppped up and the same responses happen followed by her attacking me.
I can avoid this by simply walking as far away from her as possible, and after I get & complete the mission to kill the head shaper on the islands she is fine and regards me as a fellow rebel, however it is an annoying bug.