Revealing mistake: Near the end, when the captain is walking out of the labyrinth holding the baby, you can tell it's a dummy. The baby does not move in the slightest, you can't even see it breathe.
Other mistake: The same shot of two guys looking at a computer while sitting outside on the school campus is used in two different scenes. (00:02:15 - 00:11:35)
Continuity mistake: When Hornet is pretending that Victor is trying to kidnap her, she lets go of his jacket to get away. In the following shot, she is seen letting go of his jacket again.
Deliberate mistake: When Hellboy is attacked by the spider-lady, as the spiders begin to descend on him to steal the sword, you can easily tell that some of the shots of the spiders coming down are repeated 2 or even 3 times, and simply flopped horizontally to appear different.
Continuity mistake: Arthur had only 36 hours to spend in the Minimoy world, and he leaves at midnight. He spends a full 24 hours too long as a Minimoy. After he finds the Minimoy Princess they travel during the day. They spend the first night sleeping in a flower (24 hour mark); the second night he is wandering under the house, the grandma is sleeping in a chair above him (48 hour mark). He then returns at noon. That's 60 hours.
Continuity mistake: When the monster puts down Hanso after she tries to escape, you can see her footwear is completely dirty, but in the next shot where the monster's tail uncoils itself from her body, you can now see the pink and white of her footwear that you couldn't see before.
Continuity mistake: At the garden party, when Scarlett Johansson is sitting on the bench and talking, her hair is alternately tucked in and then on the outside of the sideframe of her glasses.
Factual error: Jerry says that Flynn argued with Stephen Hawking regarding the thesis of Hawking's book when Flynn was only nine years old. However, Flynn celebrates his 32nd birthday in the movie in 2006, meaning he'd have been 9 in 1983 and 1984, while Hawking's first book, A Brief History of Time, wasn't published until 1988.
Audio problem: When the kid's dad and Santa are singing about believing in Santa their mouth movements do not match the music well.
Continuity mistake: When young Kostya is standing on the table with the jump rope tied round his neck, its knot repeatedly changes position, from Kostya's front to his back.
Factual error: Throughout the film, most Japanese words are spelled in Katakana. In real-life Japanese, however, Katakana is exclusively used for foreign words adopted into Japanese language, like 'table', 'television' (mostly it is abbreviated to 'telebi') and 'racing car'. But in the film, even indiginous Japanese words such as 'samurai' are spelled in Katakana, not - as they should be - in Hiragana (the syllable system used for native words).
Continuity mistake: After Stark fights with the Wakandians his armour is damaged, but while he is drinking on the ship the damage is repaired, then the suit is broken back again.