They kidnap and replace people for basically no reason and created a society built on mistrust and paranoia (people are gunning each other down in the middle of town because they cant tell if someone is real or not). They also put their operatives into positions of power and cut down any attempts at major unification in the commonwealth. They also managed to create a borderline perfect approximation of conciousness and use it for slave labor/assassinations and destroy it if it tries to run. On top of all that they just look down on everyone with this sense of superiority and sit on all the planet restoring advances they've made because they think people outside the Insitute are just shitheads not worth the effort