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 "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 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.