Forgive me if this has been explained already but I’ve been looking for some information as to why this is and have not found anything solid to go on. It seem stupid that the elites should be enemies with the humans when they were clearly allies in Halo 3
There are different factions among the elites. Some wish to have peace with the humans whilst others think they should finish what they started and wipe us out.
There’s a lot more to it than that. You can read more about them here.
I’m guessing that the remaining Elites are Rogues or are still faithful to the covenant, despite the events in Halo 2 and 3. You also got to keep in mind that not every Elite would probably listen to the Arbiter and his council. They might think against him and they probably still want revenge on Master Chief, for everything he has done in the previous games. Can you blame them? lol.