Carlos has a cousin, 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.
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 Julian; then the construction episode reveals that Julian is a slightly destructive toddler. Seeing how upset Wanda was when her toy was recycled, of course she wouldn't want Julian to smash it.