These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Hopper. What else can describe someone who outwardly says that he'd murder his own brother if he could, threatens to feed a scared little girl ant to his "pet", kills his own henchmen for suggesting not to go back to Ant Island, mercilessly bullies others, and practically gets off at the said bullying? Fittingly, he is also the first Pixar villain to actually die. And it's a really nasty death.
Ear Worm: The little flute-sounding song that some ants are performing for the circus bugs.
Foe Yay Shipping: Hopper and Flik. Some people couldn't explain why they kept watching their No-Holds-Barred Beatdown scene repeatedly when they were children, they sure can as they got older.
Genius Bonus: Those familiar with black widow spider mating habits might view some of Rosie's lines in a different light. See also Getting Crap Past the Radar.
Moral Event Horizon: Hopper crosses this in his first appearance and keeps on going throughout the movie. His plan to squish the queen after the ants gather all their food for him is particularly vile.
In the documentary The Pixar Story John Lasseter, and many of the other animators give off a sense that this movie is an Old Shame. One of the animators explained that they spent more time trying to make the movie better than Toy Story, instead of simply trying to make the film good in its own right.