The leper- ahem.. "plague" ship being raided, with one victim losing an arm.
Cutlass Liz randomly stabbing people. In a kid's film. What should be horrifying suddenly becomes hilarious.
Designated Hero: Why are we rooting for the pirates again? The only thing they done that's even remotely close to genuine goodness is saving Polly, who the Captain had himself sold. Let's not forget that these people have sworn themselves to looting and gutting people. They are the lesser of two evils in the story and it's a children's tale, but one can still wonder why we are supposed to sympathise with them.
Because they're amusing and it'd be a very boring world if you were only allowed to sympathise with a morally upstanding protagonist.
Designated Villain: Darwin in the first half of the film. Sure, he tried to steal Polly... After the pirates attacked his ship, threatened him with decapitation and tried to murder him for the hell of it.
Draco in Leather Pants: Downplayed. While Darwin isn't much of a villain, the fans still treat him with more sympathy than the movie itself does.
Ending Fatigue: According to the DVD commentary, the film risked this trope during production, since there were so many tiny loose ends to tie up. The Aardman team was anxious to avoid the trope, however, and managed instead to tie up all those loose ends in a Creative Closing Credits sequence.
Genius Bonus: Darwin is cataloging a new species of barnacle when he first appears. Before Origin of Species, Darwin spent much of his career systematizing the taxonomy of barnacles, and was considered one of the world's top experts on such crustaceans.
What Do You Mean, It's for Kids?: It gets pretty dark and depressing at times and there are a few mild profanities throughout. Also, the regular mention of 'running people through', plus people getting stabbed onscreen.