I think that's most likely an issue with the opposing AI-- and not just in Halo 3. Enemy AI always seems to target player characters first. When the player is the MC, at least it makes sense, but I could never figure out why the Scarab at the end of Kikowani Station in ODST remained laser-focused on the rookie, no matter where on the level he hides, and practically ignores the rest of the squad flying around in a Phantom.