Continuity mistake: Hellboy tosses Dr. Manning through the quickly-closing door to escape the pendulum on the bridge - he barely makes it under. Hellboy then spends thirty seconds dodging the pendulum, but when he dives for the door it's still closing at the same point and speed - just enough for him to pass.
Continuity mistake: When Hellboy is walking at one point, holding his gun up in his left, gloved hand (just after one of the agents has said "This place is like swiss cheese"), watch the frame. It switches suddenly so his right hand (the stone one) is his left, and he's holding the gun in his "right."
Continuity mistake: Hellboy's oversized "Samaritan" revolver is shown to only hold 4 rounds. Yet he fires at least 6 without stopping to reload during his fight with the first Sammael creature in the museum.
Other mistake: In the scene where we see Professor Bruttenholm talking to Myers about Abe's origins, we see the professor pick up what he specifically describes as "rotten eggs" from an open bowl and place them into a tube. The eggs have been sitting out in the open the whole time, but Myers only reacts to the smell once Broom picks them up.
Continuity mistake: In director's cut dvd edition, toward the end of the movie, when Hellboy hits Kroenen in a head, and says, "You killed my father, your ass is mine," Kroenen's left side of a mask changes from being damaged to intact, than damaged again from different angles.
Revealing mistake: In the scene in the alley behind the museum where Hellboy first encounters Rasputin, Sammael has its tongue wrapped around Hellboy's arm. When Myers enters and shoots at Sammael, look closely at Myers' hands. Not only does the gun fire without him pulling the trigger, but the gun does not even recoil.
Continuity mistake: At the end when Hellboy is carrying Liz off the alter she hasn't got a top on. Later after Hellboy kills the behemoth she has got a top on.
Continuity mistake: When Kroenen slices the statue, the cut where the reliquary splits in half isn't close to any of his hits; his hits are toward the upper half of the statue.
Continuity mistake: At the end of the movie, when Rasputin is about to take away Liz's soul, the shot is over Rasputin's shoulder with Hellboy's front in view. We can see Rasputin's hand move from above Liz's chest to her jaw as he bends over. Then the shot changes to Rasputin's front. In this shot, the hand is back above Liz's chest and is moving to her jaw again.
Continuity mistake: Kroenen kills the two museum guards on the balcony and they flip as they fall. The shot on Kroenen shows both landing facing up (use slowmo to see ties) and they bounce with their toes pointing up. In the next shot showing Kroenen and the other guards, the dead guards are facing down.