ApparentlyEgg Monsters from Mars didn't quite make it past the radar completely unscathed, but didn't seem like it had to change much either. The book comes off instead like a very thinly veiled analogy for female puberty, especially menstruation, and it seems all the radar made them do was change the protagonist from a girl to a boy, apparently not even changing their name (boys named Dana aren't unheard of, but it's still far more commonly a girl's name). It includes scenes of the protagonist covered in egg monsters and even laying an egg at the end.
The cover alone for My Hairiest Adventure (book #26) is just ripe for sarcastic, immature book bloggers to make jokes about the myth that masturbation causes hairy palms.
My Hairiest Adventure also seems a heck of a lot like a metaphor for puberty — he's getting weird dark hair everywhere, it grows back after he tries to shave it off...It turns out that he's actually a dog, and the serum he had to be injected with was a failed experiment in turning dogs into children.
It just can't be an unfortunate coincidence that the Doctor's name is Doctor Murkin, now can it?
Naturally, this was brought up on his 2016 AMA on Reddit. What was his response? "Maybe."
Ghost Camp (a Spiritual Successor of Ghost Beach) has a sequence where Lucy reveals to Harry that everyone in camp is a ghost and the only way to escape is to get inside a human body. The subtext of that sequence plays out like Harry is being raped.
And, on the non-sexual side of Getting Crap Past the Radar, Ghost Camp had a lot of scenes of kids doing violent things and not getting hurt (i.e., Lucy sticking her arm in a fire to get Harry's fallen hot dog, a girl getting decapitated by a soccer ball, a boy jamming a fork in his neck, Lucy pretending to drown to scare Harry, and a boy's foot getting impaled by a tent stake).
Another non-sexual example: in Why I'm Afraid Of Bees, Gary (after being turned into a bee) is at one point tempted to sting his neighbor, but refrains because bees die after using their stingers. But his life is so miserable, and his neighbor is such a despicable Smug Snake that committing suicide almost seems worth it for a second.
If an older audience reads "Piano Lessons Can Be Murder," Dr Shreek can easily come off as a pedophile (and the TV version of the episode does nothing to tone it down).
Ricky's revenge plot against resident Alpha Bitch Tasha in Calling All Creeps! is more or less the same idea as writing "For a good time, call..." on the bathroom wall.
RL Stine has said that it was indeed inspired by something like that which happened in college.
The TV adaptation has this line from a female Creep member, when the Creeps phone Ricky: "We're ready to plant the seeds."
The last leg of Be Careful What You Wish For puts in as much Les Yay as you can get away with in a 90's children's book. After Samantha wishes for Judith to become her friend, the latter instead develops what appears to be an...unhealthy obsessionfor her. Judith carries Sam's books, wears the same clothes as her, waits by her house in the morning just so she can walk to school with her, and sneaks into her room during the night.
Read Monster Blood (the first one) as an adult (or post-adolescent with an immature sense of humor) and look for the implications of puberty (the constant references to "growing" and "feeling something weird and sticky" while Evan sleeps), masturbation (one scene had Evan trapped in a bathtub of Monster Blood and the way his struggle to get out of the tub was written, it sounded like Evan was on A Date with Rosie Palms), and Unresolved Sexual Tension between Evan and Andy (who's a girl).
Also read Stay Out of the Basement, where most of the lines (when taken out of context) allude to being "in the closet," being "out of the closet," "going down there" (referring to the basement), "experimenting," and fights over paternity (the clones of Dr. Brewster arguing amongst themselves over who's Margaret and Casey's real father).
Recurring antagonist Slappy, the evil ventriloquist dummy, hits and attempts to enslave children in all of his appearances and seems to have a weird thing about twelve-year-old girls.
This comes to a head in Bride of the Living Dummy where he wants twelve-year-old Jillian to be his bride. He also punches her, proclaiming it was only a "love tap". Yikes.
In the short story A Holly Jolly Holiday, protagonist Beth and her family watch a holiday special on an enchanted videotape and fall under the spell of its main character, a cheerful pixie called Susie Snowflake. Upon seeing that her hair is starting to turn pink like Susie's, Beth tries to express her frustration but can only come out with "oh s ... ugar cookies!"
In Attack of the Jack!, Violet's uncle pretends to offer her "grog", then drinks a dark liquid he insists is diet Sprite. She wryly comments that it does not look like Sprite.
Another non-sexual example comes from Wanted: The Haunted Mask which has a shockingly graphic death scene in which William, the shopkeeper, tries to take off the mask only for his face to be torn off. The book even goes into detail on how the blood is flowing from his face as he tries to lock the mask away.
The cover of Why I Quit Zombie School has a surprisingly graphic image of a zombie kid's eyeball popping out.
In Headless Halloween, the protagonists find beer in their teacher's fridge.
The villain of Who's Your Mummy? at one point engages in an unbelievably graphic act of cannibalism, ripping out and devouring one of the raw organs of a semi-resurrected mummy. That the blood is described as being black potentially only makes the scene even grosser.
The TV Series
In The Haunted Mask II, the mask riding around in the body of the elderly shopkeeper looks at Steve a preteen and says, "Groveling. I like that in a boy."
Someone refers to Steve as "just some old drunk".
Vampire Breath sees Count Nightwing contemplating whether to feed on Freddy or Cara, which has more than a few pedophiliac undertones.
Nightwing: Where to begin? Boys have such a hearty, robust flavor. Rich and satisfying. On the other hand, girls offer such a sweet, delicate bouquet. So refreshing.
In the 2015 film, when two officers inquire about the scream heard from Stine's home and he shows them a giant surround sound TV, he says "I wasn't aware being an audiophile was against the law.", to which Officer Stevens angrily screams, "a WHAT-o-phile?!" and has to be calmed down and corrected.