Revealing mistake: In the beginning of the movie, when Hellboy is speaking on the phone with "Dad", he's speaking on on speaker, but when the phone shows up, instead of showing a screen of a call on speaker with the duration on the call, the screen shows what would appear if he was receiving a phone call before accepting or declining. (03:35:00)
Continuity mistake: When Major Ben Daimio is saying the line about putting Hellboy back in his cage, he's walking towards an elevator door mid sentence and looking at the door. The camera cuts to a different angle as he finishes this sentence and suddenly his head has turned 180° with him looking at Hellboy instantly between shots. (00:41:55)
Revealing mistake: When Hellboy is seen filing his horns towards the beginning, as he runs the file along them (right before Broom takes the file), the prosthetic horn stumps are moving up and down unnaturally for a moment. As they are meant to be protruding from his head, they shouldn't be moving up and down as he moves the file back and forth.