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." (00:59:40)redbaron2000
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. (01:30:55)Phoenix
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.
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 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: When Professor Broom is feeding that thing in the tank rotten eggs, you see him pick up one egg and put it in the tube. When he pushes the tube up in the next shot, you see more than one egg in the tube. (00:20:00)
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. (00:41:35)Phoenix
Continuity mistake: In the scene where Hellboy and his group arrive at Graveyard 16, a shot from farther away shows the graveyard in the background and in the foreground are the 3 vehicles in which they drove up. The two smaller vehicle's roof, hood and windshield are already covered in what looks like about 1 cm of snow, although they just arrived. Such light and dry snow that appears to be falling in the scene would have been blown off the car while driving, and a layer that thick takes a lot longer to develop.
Continuity mistake: In the final scene between Hellboy and Liz, when he is telling her what he said to bring back her soul, the shots change several times between one of her face, and the back of Hellboy's head, and vice versa. Every time we see Liz's face, she is looking up into Hellboy's face, but when we see the back of her head on the interspersed shots, her head is not inclined upwards at all.