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 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.
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.
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.
"Cutlass Liz" was a real-fake pirate long before this movie. That is, there were "accounts" of a female pirate supposedly named "Cutlass Liz," filled with glaring historical inaccuracies and contradicting years and just far-fetched scenarios. Long story short, "Cutlass Liz" was exactly the kind of over-the-top tall-tale kind of pirate that this movie is parodying. And this movie's Cutlass Liz seems a perfectly fitting depiction of the larger-than-life/not-very-historical figure.
Scarlett Morgan, the still-live pirate hanging at Execution Dock.
What Do You Mean, It's for Kids?: It gets pretty dark and depressing at times and there are a few mild profanities throughout. There are jokes that not-so-subtly reference sex, voyeurism, and bestiality. Also, the regular mention of 'running people through', plus people getting stabbed onscreen.