Cows
Despite the fact that cows can be fairly easily wrangled, it takes school administrators almost a year to remove the cows from Wayside School.
Elevators
All elevators are able to move up and down when they are functioning normally. However, the elevators in Wayside School, in a subversion of reader's expectations, are only able to go in one direction.
Santa Claus
All of the kids believe in Santa Claus; however, readers know that Santa Claus does not exist.
Mr. Gorf
Because of his age and his demeanor, Mrs. Jewls' class thinks that Mr. Gorf is the husband of their former teacher Mrs. Gorf who wasn't eaten alive. However, readers' expectations are subverted when it is revealed that Mr. Gorf is actually Mrs. Gorf's son.
Louis
Louis is still a reasonably young kid, yet is told by a teacher that he had to make up a homework assignment from 15 years prior, despite the fact that he wasn't alive 15 years ago.