"stir the pot" is to bring issues on the surface. Try to picture a pot of soup, with ingredients settled to the bottom, so you 'stir the pot' to bring the ingredients up.
"stir the pot between you and me" means he's trying to bring issues up that happened between you and me before. e.g. You and John had a fight long time ago, now Peter mentioned this again to you, reminding you of that the fight happened between you and John
Hope this helps.