Chiro becoming monkey-ish after Antauri died in the second season finale? Well, Antauri might had possessed Chiro's body, and...
Otto's first act after going Fake Defector in "Meet the Wigglenog" is to make everyone stop having to bounce all over the walls...by shutting down the Super Robot, which the nog in question had just set on a new course in order to begin a reign of conquest. While this obviously wouldn't have done much and more likely actually was specifically intended to make everyone stop getting bounced everywhere, it could still be seen as a hint as to his actual intentions.
When Captain Shuggazoom left the Alchemist's home, he was already transforming into Skeleton King. And the 'Hyperforce', just normal monkeys by then, were witnesses how his body slowly degraded, before he changed them into cyborgs and erased their memories. Could they have fled should the Alchemist have become violent towards them? WAS he once or sometimes, when Skeleton King realized the Alchemist would want to make them into a force capable of opposing him? We don't know and that is the most terrifying about this time.
The episode "Galactic Smash" centers around a game where players destroy inhabited planets to score points. One player, The Commodore, sets his sights on Shuggazoom, with predictable results. The problem is that there's at least 4 other players on the scoreboard, all of them with the same goal, so even if The Commodore is dead, there's at least 4 others going around the universe, doing much the same thing.