These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The arc where the girls turn evil, letting Simon take over Trollzopolis. He pulled off quite a Xanatos Gambit.
The girls stopping the Trollhiti volcano from erupting in the last episode.
Crowning Moment of Funny: In "Onyx's Gem", Onyx runs off in the middle of practice for the talent show. Amethyst tries to call her house and gets the answering machine.
Onyx: Hey. You ever feel like a freak talking to a machine? Don't let that stop you. *BEEP*
Fridge Brilliance: Why, when the Power of Ten is used on Simon and Snarf, do they not go away for good? Because, as revealed later, Zirconia and Spinell's powers had been drained during their imprisonment, so the spell wouldn't be at full strength.
Fridge Logic: So the Ancients were around the same age as the girls when they fought Simon 3,000 years ago. That means Zirconia and Spinell were either married as teens, or they were married after being transformed.
In one episode, the girls and boys are attacked by ghost dogs when the bus breaks down. The dogs, being ghosts, are intangible enough to phase through walls. They can still eat you.
The girls having to face a cyclops...without their magic. If they failed, the Ancients would die.
The walking trees in "The Big Test".
The Trollz turning evil in "When Good Girls Go Bad". Really ramped up by them freezing Coral, Opal, and Jade and manipulating them like puppets.
On the website there is mention of Black Amber (implied to be very bad stuff) and how it contributed to how things turned out. It is never mentioned in the show.
Specifically, Simon was said to have unleashed Black Amber, almost destroying the planet.
Unfortunate Implications: Garnet, who is supposed to be black, is evil. Okay, Ruby is actually half black, but very light-skinned, which makes this even worse.
Shale and Mica start out evil, too, but they reform.
Thinking about it more, Garnet may have been like that as a counterpoint to Ruby. Doing everything a bit further than Ruby normally would, including appearance. Note her hair was darker, too.