The entire introduction, which consists entirely of the narrator attempting desperately to explain how the heck the school ended up the way it did.
In the first story, Mrs. Gorf successfully turns every student into apples. Just as she's celebrating that with no students she won't need to force herself up the stairs every day, the apples attack her.
Wayside School is Falling Down
In chapter 12 of Falling Down, Jason's pencil chewing habit gets so bad he has to borrow pencils off of other students and chews them too. Mrs. Jewls' solution? Taping Jason's mouth shut. This becomes even funnier because when Allison laughs at him, Jason's speech impairment allows him to curse at her without impunity. Oh, and because of his big mouth, Jason has a lot of tape on his head.
And at the end, Mrs. Jewels notes that Jason was a lot quieter than normal, and considers doing the same for the rest of the students.
"Star bringing purple! Star bringing yorbel!STOP BRINGING YORBEL!STOP RINGING YOUR BELL!"
Wayside School Gets A Little Stranger
The confusion that "Pet Day" causes for readers who don't read the list of students and pets at the end.
And the later blink-and-you'll-miss-it Call Back in the voice switching incident.
The introduction of elevators into the school. The principal decided that there should be two elevators: one that goes up, and one that goes down, and in order to prevent kids from playing around with them they should only be able to go in those directions. The result: the elevators are used only once, and then never again.
When all the students were sent to different schools, Todd was sent to the worst school of all, but the narrator doesn't need to tell you what it was like — Todd was sent to your school.
Sideways Arithmetic Series
Todd gives the correct answer to the problem, "ears+ears=swear", but then gets told to write his name under "Discipline" for swearing in the classroom.
One of the Erics trying to wing a geography quiz by answering every question, "Alaska", and getting "at least one" correct as a result.
When Allison expresses concern that inviting too many boys to her birthday party would make it become too "silly", Mrs. Jewls "mathematically" confirms her concern by writing, "boys+boys=silly" on the board. Then, for the sake of gender equality, she also writes, "girls+girls=silly".
Mrs. Jewls makes multiple attempts at trying to remember her computer's password, but each guess only delivers the message, "That is not the password." Eventually, she becomes so desperate, she also types, "That is not the password." That doesn't work, either.