This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The ClueFinders
The Medusa rock with snakes coming out of her eyes in 3rd Grade Adventures.
Any given part of Goo Lagoon in 3rd Grade can be this to the squeamish, and kids tend to freak out at the extremely Beatles-inspired song.
Try "Do You Believe in Monsters?" in the Monkey Kingdom. The red and black animations are really good at looking creepy. Even worse, the animation shows Mothra carrying off a cub.
The aliens in 5th Grade.
The reading comprehension task - it's actually kind of freaky despite being pretty innocent. Reading the cryptiles shows a bit of desperation from people who're afraid of the island and are trapped there with no way to escape.
The Revealthat they eat brains, and that they've captured everyone you've met on the island (and countless other people who sailed near it) to that end. Including Leslie's grandfather, which you see in a Jump Scare with a Scare Chord no less.
Furthermore, where you try to access the map inside the ship, LapTrap says, "Sorry! But we are now, trapped, inside!"