When Bart and Lisa tumble into the creek, you can tell its pretty deep from the underwater shot of them choking each other. But when they resurface they're able to stand and the water's only waist deep.
On the field trip memorial wall when Willie has to enter Bart and Lisa's names, you'll notice 2 particular names. El Jefe (Hefe) and Fat Mike - horns/guitar/backup vocals and bass/lead vocals/founding member (respectively) of the punk band NOFX.
Bart's fanny says "Lisa's Brother" and Lisa's says "Bart's Sister."
After Lisa is given her paper, you can clearly see that there is a B+ on top of the stack of the papers the teacher is holding. But a moment later, she gives Bart an A!
Principal Skinner breaks the fourth wall in this episode, saying "If this episode has taught us anything...".
Bart says that when he gets through with Lisa's flag, "it's gonna be a Bart-mangled banner." "Bart-Mangled Banner" will eventually be the title of episode 334.
The DVS narrator is different in this episode only.
A common misconception about this future episode is that Bart fails the third grade. Something impossible for 4th grade students like Bart.
This episode implies/confirms that Illinois is actually Springfield's State (and this needs to be canon), which we can tell by where the beam from the satellite dish was coming from (just southwest of Lake Michagan). This also proves that Springfield is most certainly not in it's own fictional state like David Silverman claimed it to be (the one known as North Tacoma).