Warning spoilers everywhere
Mostly Peter turning into a cult leader. Like they didn't offer any justification, but the old big bad got shot down so they needed a new one and eenie meenie minie OH HEY Peter you get to be the new psycho of the show with no in universe explanation or anything. Also for some reason Amy didn't get killed like every other living thing on the island? She just got disfigured? What in the crap.