- The episode "Creepy Crawly Campy" could be considered Nightmare Fuel, since it was most likely intended to be scary. The fact that it's a kid's show is the only thing holding it back.
- "Meatman", especially the ending where it's heavily implied that Meatman killed Lazlo, Raj, and Clam and morphed into duplicates of them so he can eat the other Bean Scouts.
- The yetis breaking into the radio station in "Radio Free Edward". It veers into Nightmare Retardant once you find out that the yetis are a nice, intellectual couple of guys, but Edward's terror is infectious.
- At the end of "My Brother's Eater", Skip tries shoving Edward face first down Chip to retrieve a flashlight. Edward's muffled screams of anger are enough.
- In "Float Trippers", Raj is depressed that he lost his retainer on the last day he needed to wear it. He wants perfect teeth and not to end up like his brother with jagged teeth and tusks. Said brother had ran away and worked at a circus as a freak because of the shame. The REALLY creepy/scary part is how Lazlo congratulates Raj for (mistakenly) rejecting to get his retainer back just as it floated on by, that he doesn't need perfect teeth to be happy, and that he would be content to one day look like his brother. Lazlo shows a picture of his brother again... only this one has one of his tusks grow and curl in a way that stabs his eye.
- Hilarity aside, Tomato Paste ends up having unsettling levels of nightmare fuel when faced with the prospect of being promoted from a Bean Scout to a Tomato Scout. As demonstrated by Commander Hoo-Ha, Tomato Scout recruits endure agonizing rituals of being pelted by tomatoes and essential torture in various other ways until they're hardened into becoming vicious anger-prone military types like Hoo-Ha himself. Hoo-Ha actually laughed while showing Edward the slideshow of recruits crying in pain and terror from the rituals. Keep in mind becoming a Tomato Scout is meant to be a reward for achieving all the Bean Scout merit badges. If it is found that a scout cheated to get the badges like Edward was revealed to have done the scout gets sent to Camp Skull Crush as punishment. It is never explained what happens there but the name of the camp says volumes.
- Worse is that Hoo-Ha implied the traumatic events of becoming a Tomato Scout would forever mentally scar the recruits by giving them PTSD. As he puts it: "Tomato Scouts never leave the war zone!"
- Commander Hoo-Ha appears again as the source of Nightmare Fuel in Valentine's Day. He reveals to be such an Overprotective Dad to his daughter Patsy that the mere thought of her liking a boy or vice versa (especially vice versa!!) sends him into a murderous rage. When he finds the Valentine card Patsy made for Lazlo, he decided to torture the Bean Scouts with a series of physical tests until they told him who made the card and for whom after which the culprit would be personally beaten and punished by Hoo-Ha for eternity. The last test involved all the Scouts getting beaten into traction by Patsy to find the boy she wouldn't hit so Hoo-Ha could maul the boy like an animal. He did all that to children just for the thought of any romantic interest in his daughter.
- The ending of "Call Me Almondine", where the Squirrel Scouts remove their prosthetics and wigs to reveal they were wearing them to hide deformities and missing body parts. While most likely intended to be a heartwarming moment by having the girls embrace who they are and not caring what people think, it just comes off as creepy and unsettling, especially with Gretchen removing her glass eye from her huge eye socket and another being shown to wear a fake snout over her disfigured face.
- In "7 Deadly Sandwiches" Scoutmaster Lumpus has made a hemlock berry sandwich for Jane Doe while she watches the play, then Dave arrives, playing the last and most poisonous sandwich of them all, a hemlock berry sandwich. And Jane almost eats hers. Daves Large Ham acting actually adds to this.
- Lumpus during his Sanity Slippage moments comes off as creepy, especially when he shows how he has no issue doing harm to the Bean Scouts. Becomes Fridge Horror in the finale when it is revealed Lumpus is actually a dangerous criminal who captured and hid the real Camp Kidney Scoutmaster while acting as an imposter for the entire show. Suddenly Lumpus' bouts of crazy are given a darker light and the show ends of the revelation that a camp full of children was being controlled by a dangerous psycho!
Nightmare Fuel / Camp Lazlo