Either:
1. You're playing Art/Essence of War, which, depending on which faction you play, has one other faction not have galactic AI, since having them all active would mean the EaW unit selection freeze bug would happen way too early and often. Every other faction should be working normally though.
2. You have AotR/Republic at War installed, which puts their AI changes into the base Data folder and can therefore break the AI for themselves, the base game, and any other mods until you remove the AI and Enum folders they install.