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.
Accidental Innuendo: When Pim first shows up at Wack Lizardi's office with the bag, Wack asks "What in Zill have you got to be excited about? Did someone invent enlarging pills?" (It's meant to be a crack at Pim's height.)
Alternate Character Interpretation: Oriana's second dance in the film is just her flailing her arms and spinning in a circle. Considering this was when Felix had hatched an escape plan, she may have been "dancing" like that to make sure no one really paid close attention to Felix.
Anticlimax Boss: How does Felix end up defeating the Master Cylinder? He throws the Book of Ultimate Power at him. Yes, really.
Anvilicious: The ending, as well as the book which is revealed to consist in its entirety of "Truth, Love and Wisdom". The Duke did not take it well.
Don Oriolo recently released a small soundtrack from the film on iTunes, including complete versions of the two songs mentioned above.
Cult Classic: Sure, there's a lot of problems, but it's so impressively weird that it has a small following even now.
Designated Evil: We're never told what the Duke of Zill originally did to be banished from the kingdom...his only "crime" that we're shown was creating the Cylinders, which he thought would revolutionize labor. He was jealous of the king, who he considered weak and backwards, but there's no indication that he was planning to take over the kingdom before he was banished. Oriana does state that he wanted the Book of Ultimate Power though, so he may have only been using the "labor robots" to plan a coup.
Ear Worm: The Zill national anthem. It has a terrible rhyme scheme and a huge ego, but you can't fault a villain who has a hard rock national anthem.
Who is the boss?
The Duke of Zill of course!
Who's never at a loss?
The Duke of Zill of course!
Ensemble Darkhorse: Wack Lizardi is pretty popular amongst the fandom. Some given reasons for this include that his voice actor is completely hamming it up thus making him at least slightly enjoyable to listen to, he tells Felix that he's "no good with jokes", something a fair amount of viewers agree with, and seems to actually do more things on-screen than the Duke of Zill does.
Grumper also appeals to many people who see him as the Only Sane Man.
Fridge Horror: As pointed out in part four of this review, when the circus tent collapses, you can clearly hear people screaming. After that, Progress City seems to be completely void of any inhabitants as the protagonists are trying to escape.
Pim somehow found an unoccupied boat not too far away from where the headhunters were. Unless it somehow belonged to one of the headhunters (which seems unlikely and would just bring up more questions)...
Fridge Logic: It was established early on that Felix's magic bag only transforms for him and it reverts back to normal when someone else touches it, so how come later on in the movie both Princess Oriana and Wack Lizardi were able to touch it without having it change back?
Nightmare Fuel: The opening Felix head, as well as Oriana being chased by the Cylinders early in the film.
The trees which sprouted what were essentially black and pink flying jellyfish.
The circus, especially when Who is the Boss? is performed. Also, Wack Lizardi. Just... Wack Lizardi.
Grumper's violent facial expressions
Padding: Quite a few scenes, but special mention goes to the tapdancing Mizzards scene.
Squick: Some reviewers have noted that the Duke of Zill seems to be too interested in seeing his niece dance night after night.
They Just Didn't Care: It would explain why the plot is such a mess, the numerous animation goofs that they didn't correct, and why they didn't even bother to release it into theaters until a year after it was "finished".
Uncanny Valley: The Princess, especially when she's giving Felix exposition in her room. Her eyes are staring at the exact same spot and seem to move independently of her eyebrows and jaw, leading to some freaky expressions...or her looking like she's high.
To be fair, she was Rotoscoped, which has a high probability of going incredibly wrong.
Pretty much the whole movie; the highly inconsistent quality of the animation doesn't help, and a lot of the characters move or look around awkwardly in most scenes.
Also, the computer-generated talking head of Felix at the beginning of the movie....
Viewer Gender Confusion: The Mizzards. It doesn't help that they keep mixing up which one is the pink one and which one is the blue one.
What an Idiot: The Princess dismissed her entire army because...?