Hellboy is fireproof. He isn't affected by fire in any of the scenes in the whole movie. Yet after Hellboy emerges from under the train in scene nine, he touches his stunted horns which are now scalding hot and reacts in pain.
Flubbed line. When Abe Sapiens reveals a number of facts about Myers, Myers is then supposed to say, "how did it ..." and subsequently be corrected by Prof. Broom, "he, Abe's a he." The subtitles have him saying it but if you listen Myers says "he" in the first place.
When we're first introduced to Liz it is clearly Halloween. Another woman points out the window behind Liz and says there's a big red man down there. In response the doctor says Santa doesn't come for another month.
On the Bridge scene under the graveyard, Tom Manning is thrown and slides under the door just before it closes. However Hellboy also slides under later in the scene when the door should have already been closed.
In the library, when Hellboy was walking into the crime scene, there were only three glass display cases in the center of the room, but when the monster threw Hellboy through the cases, Hellboy crashed into four cases before hitting the window
In Grigory Rasputin's lair, Hellboy and Manning are proceeding slowly and carefully through a narrow passage lined with spikes, not only to make it through without being hurt by the spikes, but to sneak up on Kroenen, who is sitting in a chair in the room at the end of the passage listening to music. Manning negates the possibility of either of these things happening when he cuts the back of his left hand on a spike and exclaims "Ouch!", which Kroenen hears. However, when he and Hellboy make it into the room and see that Kroenen is no longer sitting in the chair, Manning says to Hellboy "Hey, it really went deep", and shows him the bloody cut, which is now near the tip of his left index finger.
In the subway station fight, Hellboy fights the monster as the train comes into the station and leaves again. In a shot a minute later, the monster swings its arm at Hellboy and the reverse shot shows the train passing behind Hellboy again. However, in shots before and after, there was no second train on the heels of the first that passes by for a split second. The shot must have been moved from the prior sequence.
When Hellboy stops the car by slamming his hand into the bonnet and flips the car, the grille and bumper are seen to break off the front and as it flips over the grille about to fall on Hellboy, but when the car lands the grille and bumper are nowhere to be seen.
Hellboy escapes from both Liz's explosion and the final boss attack with clothing intact. While he is invulnerable to fire, he isn't immune to damage and neither is his clothing as it rips and shreds (clearly seen near the end of the movie where he shrugs off his slimed, torn great coat, but noted in other scenes in the movie as well). It all should have been blown to pieces during both explosions, but he arises from them fully clothed.
When Kronen is first seen, he raises his arms and his blades rotate around like clock hands, from mechanisms obviously on the outside of his sleeves. Later, when he tries to retrieve the grenade, he clenches his right fist and the right blade retracts straight up his forearm, the mechanism beneath his sleeve.
In the scene where Myers and Hellboy take cover from Samael behind the dumpster Hellboy's hand has no stinger on it when he hands the Samaritan to Myers. But when he reaches back to grab the gun the stinger is suddenly there.
When Agent Myers talks to Professor Bruttenholm about how he's not right for the BPRD he's wearing his casual clothing from earlier in the film. In previous and subsequent shots he is wearing a black suit.
Just after the opening credits we see what is later revealed to be Ilsa, Kroenen and a guide in a snowy, rocky setting which is described as "Birgau Pass, Moldavia" in the caption - Birgau, or Borgo (a popular location in vampire lore), is in fact in Romania.
The shadow of the Earth on the Moon is the same diameter for the eclipse. The Earth's shadow is much larger and would inscribe an arc on the moon aside from the Lunar eclipse taking hours instead of minutes.
Broom mentions Adolph Hitler as being a prominent member of the Thule Society while explaining the origins of the BPRD to Myers. As far as is known Hitler actually went to great pains to distance the Nazi party from the Society which was publicly dissolved well before Hitler ever came to power.
When Ilsa offers the gold to the Russian general in the freight container with the Tunguska artifact, she presents the suitcase with one hand. However, this amount of gold would be too heavy to be lifted with one hand - at least for a woman of her stature.
The Caprice taxi that Liz and Myer are riding in has its rear windows rolled all the way down. This is not possible for those model years of Caprices as the way the door is shaped prevents the windows from going all the way down.
The character name of "Abe Sapien" makes the usual mistake of shortening "sapiens", which is already singular. Even the fanciful taxonomy of "Ichthyo sapiens" shown before his name is revealed uses the correct form.
After Red throws Manning under the closing door and the causeway begins to crumble under his feet, Hellboy is obviously being suspended on a trapeze since the bricks under his feet are dropping and he is staying elevated and flailing about as opposed to falling or moving forward. You can see when the camera goes to a behind the back shot, that the collar on his coat is perked up, indicating that there is a cable supporting him which was digitally erased in post-production.
Whenever anyone fires an automatic pistol in the film, as when Myers shoots Sammael in the alley, there is no rearward action of the slide, no ejected shell casings or apparent recoil, and the muzzle flash is obviously superimposed, because the shooter is not illuminated by it. The only exception is agent Clay's gun when he is shooting at Kroenen, which in fact is a blank-firing weapon - the gun even locks empty (slide back).
When Kroenen is fighting off the guards during the museum scene, as he moves his arms around, the knife and sheath on his upper arm bends and twists significantly, revealing that the prop is made of rubber and fiber-glass.
Underground, just after Abe is injured underwater, and the two agents are killed, Hellboy is walking into a room. As he enters, his RIGHT hand is normal and holding his gun. Just after he approaches the table, now, his LEFT hand is normal and holding the gun. His large hand has changed sides.
The goof items below may give away important plot points.
At two different times, it is stated that six guards have died in the museum. Yet, when Abe shows Professor Broom what happened, we see seven guards killed by Kroenen. Two on the catwalk and five on the floor with Kroenen.
Before confronting Broom at the BPRD, Kroenen wound the mechanism in his chest counter-clockwise, which should have caused him to deactivate as it did when he wound it counter-clockwise before Hellboy finds him in the tunnel. In all other scenes he winds it clockwise before he sees action.
At the end of the movie, any shot of Liz laying on the altar shows that she is clearly lying under a blanket, by the way the cloth drapes over her and extends over the altar. After Hellboy's fight with Behemoth, the blanket has changed to become a strapless dress, with slightly different embellishments. If it were still a blanket, it would have fallen off Liz when she first stands up, because neither she nor Hellboy makes a move to keep it in place.