The inhabitants of the "plague ship" are clearly lepers, and were named as such in the trailer. The word leper was removed from the finished film after complaints by a Leprosy charity organization.
When Queen Victoria tells the Pirate Captain that "I may have the heart and soul of a weak woman" she is quoting from her predecessor Elizabeth I, who made a very similar remark in a famous speech in 1588 when England when threatened with the approach of the Spanish Armada.
Brian Blessed is printed above the tick box representing the best choice for 'Roaring' at 'The Pirate of the Year' awards. Blessed performs the voice of the Pirate King.
When Charles is describing the new species of Barnacle he discovered, he is seen with his back facing his collection of animals. In the next shot, the animals are to his right.
When Black Bellamy arrives at Blood Island in the whale, Pirate Captain and Pirate With A Scarf walk to the hole in the wall and witness the whale jump from the sea. There is no table behind them, but when the whale bumps into the building, a table and occupant have appeared for its mouth to drop open on.
The pirates' ship heads to London and stops in Calais for some duty-free shopping. Calais is misplaced on the map. It should be far up north, above the word "Flanders".
Yes, the film is based on the first two books from Gideon Defoe's 'The Pirates!' series - 'The Pirates! in an Adventure with Scientists' and 'The Pirates! in an Adventure with Whaling'.