Accidental Innuendo: The episode covering plants features a scene where Wanda gets hit by "white stuff" ejected from a chloroplast that's "gooey and sticky"note it's sugar, thankfully and is subsequently grossed out by the fact that it lands in her mouth before she finds out that she likes the way it tastes. Children's educational television, everybody!
Adaptation Displacement: The TV show is better known to some than the original books; in fact, a new series of paperbacks went into print based on the TV episodes.
Is Ms. Frizzle something like a Willy Wonka who is teaching the class to find a successor to the Magic School Bus?
Is Ms Frizzle a normal human or not? She's implied to be older than her roughly 30-to-mid-40s look, and she is into magic.
Is the school bus really magic or is it science? Or perhaps both? It's an oddity that a science teacher would be involved with magic. Clarke's Third Law comes into effect.
Base-Breaking Character: Tim is this mostly for being The Generic Guy—he's not hated, per se, but he doesn't have as big of a fanbase compared to the other characters (but he does have some fans).
Cargo Ship: Who's the fandom's number one Frizzle-related ship? Arnold or one of her other students? Someone's OC? Mr. Ruhle? One or more of the producers? Lizzie? No, don't be ridiculous - it's the bus, obviously.
A theory among the LGBT Fanbase suggests that Ms. Frizzle is Arnold from the future, post-gender-transition. The similar hair, Ms. Frizzle's absolute unflappability, her fondness for pickles... Pickles? Spironolactone, an androgen blocker commonly taken by trans women in the US, is also a potassium-sparing diuretic, resulting in increased thirst and cravings for salt. Pickles solve both of these problems, and have become a meme in trans communities as a result.
Fanon: Her traveling through time, space, and dimensions with a group of students in a shape-changing vehicle has led to the nigh-unanimous fandom consensus that Ms. Frizzle is a Time Lord.
In "Out of This World," aired years before Pluto's demotion, the class is rehearsing a play about the solar system where they each play a different planet, but Dorothy Ann is late, so they had to start without her planet... Pluto.
Launcher of a Thousand Ships: Arnold. He's been shipped with everyone - everyone in his class, Ms. Frizzle, Molly Cule, that guy from the hot cocoa episode (Harry Arm), that girl from the water cycle episode (Tiffany), Janet, Azula...
In Israel, the show was just called The Magic Bus (because school buses are not as ubiquitous there). Unfortunately, magic (or, more accurately, acts of magic) sounds a lot like drugs in Hebrew (קסמים ksamím vs. סמים samím, respectively). Cue many jabs from kids whove outgrown the series about the bus adventures being a case of Mushroom Samba.
The episode in the sound museum is also pretty creepy, with the class staying overnight in a vast and seemingly-abandoned building with some very surreal features and chasing after the sound of mysterious music that sounds rather creepy in its own right.
Paranoia Fuel: If you're sick, a science class might enter your body in a shrunken bus to find out why.
That One Level: The platforming minigames in the Explores the Solar System computer game all can be fairly difficult, but the Saturn level with Tim is generally agreed by people who have played the game to be the most frustrating one. The level takes place on tiny slick platforms in Saturn's rings that you will almost constantly be sliding off of into a level-wide Bottomless Pit (causing you to start over) until you get a jetpack a few screens into the level. While the jetpack can keep you from falling into the bottomless pit, it also uses up air. Running out of air will also start you over, without the jetpack, meaning you have to navigate Saturn's icy platforms to get it all over again.
Periphery Demographic: The series has gained a large amount of older fans, many of whom grew up with it. It helps that both the facts (for the most part) are still relevant and the characters are interesting. Older fans have been known to revisit the show because of how much they forgot that they had learned in elementary.