Character mistake: When Arthur Weasley takes Harry aside in The Leaky Cauldron to warn him about Sirius Black, he says, "13 years ago, when you stopped.... You-Know-Who...Black lost everything." Harry is 13 yrs. old in Prisoner of Azkaban and was a 1 yr. old when he stopped Voldemort. Hence, Harry stopped Voldemort 12 yrs. ago, and not 13! Harry turns 11 just before school starts in Philosopher's Stone, turns 12 before school in Chamber of Secrets and turns 13 yrs. old before school in Prisoner of Azkaban. Just an aside, the last digit of Harry's age always coincides with Harry's year at Hogwarts. So, he's 13 in his 3rd year at Hogwarts, which is entitled Prisoner of Azkaban. (00:17:50)
Character mistake: When we first see Sophie her body was slumped over (the spell to make her old) but later on in the movie, her back magically seems fine. (00:00:01 - 01:50:00)
Character mistake: Tom Manning criticises Hellboy for using a lighter, (correctly) telling him to use a wooden match instead. But he then lights a match and immediately puts it to the cigar, instead of waiting for the sulphur to burn off and using a pure wood-fuelled flame to light it. He's not as well informed as he thinks.
Character mistake: Jenna has Sparkle letters at her work. Wouldn't she get caught earlier?
Character mistake: Flynn has been reading for a while, taking notes, spreading books around, etc. - when Nicole arrives and says that it was nice to watch take-off from the cockpit. The plane must have been in the air for a long time by then.