Treasure Planet - The rebellious boy in the supermarket resembles the movie protagonist, Jim Hawkins.
The title is a parody of an earlier episode title "Bart Gets an "F"", which was parodied earlier in "Bart's Dog Gets an F" and "Bart Gets an Elephant" and would later be parodied with "Bart Gets a "Z"". The title is ironic, seeing as despite the fact that Lisa does get an "A", she cheated. The ending of the episode was also similar to "Bart Gets an "F"", where Lisa tapes the test with an "F" on it, stating that is her true grade that she deserved.
During Lisa's daydream that she has failed to qualify for Harvard University and now must consider Brown University, she ends it by chanting "Brown, Brown, Brown" as she returns to reality. Ian Maxtone-Graham inserted that as a joke, as he is a graduate of Brown University, while many other Simpsons writers are Harvard graduates.
In the Oscar Meyer's periodic table, the element molybdenum replaced by "bolonium".
Aside from bolognium, the rest of the Oscar Meyer periodic table appears mostly unaltered, except for being truncated on the right side. One notable exception is tungsten (W), which is changed to We on the periodic table, possibly signifying some version of the word "weiner".
The subplot about Homer having a lobster for a pet was similar to a Garfield & Friends episode titled "Maine Course".
Homer and Pinchy together weight 300 pounds. That's most likely a reference to King-Size Homer where Homer (but without the lobster) weighted that much.
In the opening church scene, Maggie does not have a mouth.
Wendell can be seen with brown hair early in the episode.
When Chuck is seen in class, at one point, his shirt is lavender.
Two kids in the middle of the class (a boy just behind Ralph and a girl two desks behind Lisa) do not have test sheets, however they are shown writing on their desks.
In the same scene, the globe's colors are inverted: the continents are blue and the oceans are green. Both errors can be seen in the screenshot to the right.
Lisa starts off barefoot when playing the PlayStation game. However when Ralph comes to see Lisa, she is wearing her aqua-green slippers. Then, after he leaves and she drops the book on the floor, she is barefoot again.
In this episode, Otto Mann's headphones are blue instead of their usual red.
A person doesn't catch the common cold from very low temperatures alone.
Principal Skinner calls Lisa to his office to, quote, "discuss the results of yesterday's test" except she got her grade back for said test the day before, which would mean the test would have had to be at least two days ago.
Homer states that he according to his driving license weights 140 pounds but in fact he (which is even written on the license) weights 239 pounds. So in that case Pinchy would weight 61 pounds. Also he states that Pinchy must weight 160 pounds but if Pinchy were heavier that Homer then Homer wouldn't be able to lift him.