Factual error: When Liz and Abe's plane crashes, it sinks far too quickly to be realistic. Also, from the sheer amount of force the plane hit the water with, both should easily have died. Obviously done for dramatic effect, but still a mistake.
Trivia: When the "Dragons" are being released around the world, you see a baby carriage nearly falling into one of the cracks that forms in the ground, only to be saved at the last minute. The baby-crying sound effects were actually provided by Selma Blair, who does the voice of Liz Sherman (and also played her in the live action film), after the makers realized she could do a perfect impression of an infant crying.
Trivia: The scene where Hellboy battles the vampiric heads is taken directly from one of the stories from the comic book, entitled "Heads." It was faithfully recreated when Mike Mignola and the writers realized that the story would be perfect for the semi-episodic nature of the film, and the Japanese-themed tone.
Trivia: The concept of "Sword of Storms" having to do with Japanese mythology is actually based off an early concept Guillermo Del Toro had for the live-action "Hellboy" movie sequel. However, after plans changed and the idea was dropped, Mike Mignola (creator of the comics) and Tad Stones (co-director of the animated Hellboy features) decided this would be perfect for an animated feature. And so "Sword of Storms" was born.