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.
The portraits with the moving eyes at the beginning? Never explained, beyond a vague implication that Manzini is fond of collecting magical items.
The reference of the Garbage Pail Kids being aliens through the implications of the trash spaceship.
Arguably, the part where the Kids break out in song, since there are no other musical scenes in the movie, and this music sequence comes out of nowhere in the middle of another scene.
Designated Hero: The Garbage Pail Kids are clearly just as much horrible if not worse than Juice and his gang; they terrorize the neighborhood on a daily basis with their unpredictable antics and obnoxious behavior with absolutely NO motivation whatsoever other than being nasty for the sake of being nasty. They don't treat Dodger any better, yet he's trying to make some sense out of them. They even share the bullies' taste in fashion!
Captain Manzini is intended to be the Big Good, but the most heroic thing he does is spring the Garbage Pail Kids from prison... so that he can imprison them again inside a trash can.
Jerkass Woobie: Tangerine uses Dodger and the GPK to make herself look good as a fashion designer and even ends up betraying them. At the same time though, one could feel sorry for her: it's implied that Juice is abusive as he does rough her up at times in the film.
Nausea Fuel: Given how disgusting the source material was, not surprising.
The Garbage Pail Kids themselves. They probably didn't intend on making them so horrific-looking, but they are.
The whole concept of the State Home For The Ugly.
Padding: There are several long, dragging scenes of the Kids interacting. Typically scenes like this would be used for character development or exposition, but in this movie a lot of the dialogue scenes contribute very little to the film's story. Particularly of note is a three-minute sequence of the Kids playing a prank on a random man by redirecting a sewer pipe into his hot tub.
Rooting for the Empire: As... idiotic as the idea of the State Home for the Ugly is, the fact that they want to apparently outright murder the obnoxious protagonists actually makes some people want to root them merely for that reason alone.
Snark Bait: The only reason most people who are well-informed about this movie might want to watch it.
Special Effects Failure / Uncanny Valley: The Garbage Pail Kids are little people in horrible, horrible rubber outfits. The suits are so badly designed that their mouths can't even close. Your dreams will be haunted.
The ship at the beginning of the film is a model that clearly looks like a "not-quite finished" model in front of a half-assed painting of Earth.
Squick: Tangerine and Dodger hitting on each other. She is in her twenties (or, at least, looks so) and he is fifteen.
Shockingly, Tangerine's actor is only a year older than Dodger's
The Kids themselves who fart, piss and threaten people every other minute despite wanting to be acknowledged and one even has a knife. They are just nasty in every sense of the word.
What Do You Mean, It's for Kids?: This film got away with a PG rating and is based on a franchise popular with boys aged 9 and up. However, amongst many, MANY other things we have underage drinking, thuggery, assault, a few curse words, near-nudity and implied genocide, sexual abuse and murder.