At one point, Lisa says that Milhouse likes "Vaseline on toast," a possible reference to the song "She Don't Use Jelly" by the psychedelic alt-rock band The Flaming Lips - "She'll make ya toast/she don't use butter/she don't use cheese/she don't use jelly/or any of these/she uses Vaseline."
Principal Skinner calls Nelson 'The bottom of the barrel'. However way back in "The Telltale Head" it was Jimbo Jones who Bart said needed no introduction as "the worst kid in school".
In Lisa's music class, there is a wide shot of the entire class. Üter sits next to Milhouse Van Houten in this shot. However, in the next shot, it's Ralph Wiggum. In a following shot of the entire class, it is Üter again. They both replace each other in the same seat (i.e. Ralph is nowhere to be found in the shots with Üter and vice versa.)
The hole in Nelson's locker appears to increase in size.
If Kearney has a car (the Hyundai that Chalmers and Skinner tried to steal the "H" from), why does he take the school bus? It is possible that he takes the bus if he can't use the car (maybe he shares it with someone) or that he stole the car.
In this episode, Nelson mentions that Lisa is the first person to come over his house ever since his dad went nuts, but "A Milhouse Divided" established that Nelson's dad left his mom after she got hooked on cough drops (and later episodes establish that Nelson lives with his mom, even though his dad appeared in "Bart Star" driving Nelson to Hooters [with Nelson saying that he doesn't want to bother his mom at work] and "Sleeping with the Enemy" revealed that Nelson's dad went missing for all these years because he was mistaken for a carnival freak after eating a candy bar and suffering an allergic reaction to the peanuts in it, to the point that he looked like a carnival sideshow freak and was forced to join one.
In Lisa's music class, Janey was animated joining in on the class teasing Milhouse by saying "Milhouse likes Lisa" before saying he does not like her. Also, Uter is animated joining in on the class teasing Janey by saying "Janey likes Milhouse" before saying she does not like him.
When Principal Skinner ordered a locker-to-locker search, he had Groundskeeper Willie open the lockers with a crowbar which damages the lockers. As principal, shouldn‘t he have a locker key or ask the students to open their lockers if he dosen’t know the combinations?