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.
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.
The wind blows from the back to fill the sails and pushes the ship forward, but wrongly the flag points back as if the ship advances against the wind. Aesthetic, but an inaccurate goof even seen on some classic paintings.
The movie is set in the time of sailing ships, but in the final fight scene when Pirate Captain and Queen Victoria are fighting, Captain Pirate starts falling towards a spinning propeller. Sailing ships don't have propellers.
After the Pirate Captain falls asleep in Darwin's house, Number Two is seen flicking a light switch. Electric light wasn't even demonstrated in London until 1848, eleven years after the film is set.
The Pirates disguise themselves as Girl Guides. The Girl Guide movement wasn't founded until 1909, eight years after the death of Queen Victoria.
The Pirate Captain steals a penny-farthing bicycle, not invented until 1869.
Queen Victoria's look for this movie is older and even her voice actor Imelda Staunton was 56 years old by 2012, however in 1837 Queen Victoria was 18 years old in the time of her reign.
During the opening credits sequence, a modern political division of America is shown, however in 1837 some of the states shown (California, Arizona, New Mexico, etc.) were part of Mexico yet, even California, Arizona, Nevada, Utah, Colorado, and Wyoming were a sole state called Alta California.
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".