Carlos has a brother, Mikey, who is in a wheelchair. Despite that the Frizz could easily fix any disability he has, he is still wheelchair bound. Actually, this is a stealth aesop - Ms. Frizzle not "healing" Mikey is teaching the class to accept people the way they are.
The same can go for Phoebe's father - one episode reveals that he is blind, but the characters don't comment on it. Frizzle could easily heal him - but she doesn't, because again, she's teaching the kids to accept people the way they are and he (and Phoebe) has learned to accept that he is blind.
Wanda in the "Magic School Bus Holiday Special" reveals that she's eager to donate an old toy soldier she's had since childhood to both make another kid happy and to see The Nutcracker. It seems odd that she wouldn't give it to her brother William; then the construction episode reveals that he is a slightly destructive toddler. Seeing how upset Wanda was when her toy was recycled, of course she wouldn't want her baby brother to smash it.
The acceptable break from reality in "Gets Programmed" actually makes a bit of sense in-universe - Mikey doesn't read the program back the way it was actually written, he read back what the results were because he knows that the others would not understand it - he doesn't understand specifically how a computer works, but he knows about how to program them.
In the beginning of "Ups and Downs", we know Wanda's mother is a science journalist, and she's the one who initially calls out Gerri Poveri as someone who would do anything for a story, even if it means making it up, and she sounds very certain about this. Professional opinion of someone else's reporting habits? (Maybe she's even dealt with Gerri professionally before, enough to form an opinion about her ethics.)
Arnold's head turned into a block of ice on Pluto, so that Janet had to drag his limp body on the bus. Just what did Ms. Frizzle do either on Earth or on the bus to heal him mostly so that he only had a cold?
In the "All Dried Up" episode, did their parents even know that their kids would be gone overnight?
Going on that, Arnold in "The Magic School Bus in the Haunted House" mentions that they got permission slips to spend the night, but that the slips didn't mention "haunted houses". So just how often does Ms. Frizzle remember to include that?
In "Butterfly and the Bog Beast" just how would Janet have reacted if she had realized that the butterfly she caught and planned to feed to the "bog beast" was actually the class shrunken and changed into a butterfly? (The class leaves that bit out when they finally change back and pick up Janet from where she's fallen in the mud.) If the bog beast had been a real thing and not actually just a butterfly with bright coloring, Janet could have easily fed her own cousin to it. Janet may be a Jerkass but she freaked out when Arnold took off his helmet on Pluto for her, knowing it was her fault that he made that decision. How would she have lived with the guilt that her own bullying and greed led to several students and an adult dying?
In the episode about the city and the animals living in it, it's implied that this was done on a whim - meaning their parents would easily not know where they are, only that they are late getting home.
In Out of This World the bus deflect an asteroid by increasing its own size so that its gravity will change its orbit. The sudden appearance of an object the size of the moon in Earth's orbit would cause major problems (i.e. tides going out of whack) just by being there. Nice Job Breaking It, Hero!doesn't even begin to cover it.
Janet's manipulation talents get particularly horrifying when you realize that despite the fact that she does care about Arnold, she's perfectly willing to use him in schemes to bully said friends (the "ghost in the theater kidnapped Arnold" scheme in the light episode comes to mind) or turn not just him but the entire class against one of their own just on a whim (when she suggested Phoebe was sabotaging the soccer team because they were playing her old school in the butterfly episode). Considering she's not even a teenager yet, this tendency is...worrying, not just for her but for everyone around her, to say nothing about what it implies about her parents and how they raised her.