Van Helsing throws Igor on top of a rock and interrogates him. When he lifts Igor off the rock, you can briefly see several sheets of white paper, stapled or paper-clipped together, on the rock. It's probably a script left there by the actors.
When Van Helsing and Anna are fighting the vampires in the village, when the sun has just come out, and they hear a noise from the well Anna bends over to pick up her weapon from the ground. As she picks it up it makes a metallic scraping sound even though there shouldn't be anything metal in the ground for it to scrap against.
Carl, at least twice in the movie, indicates that he's not a Monk but "just a Friar," the implication seeming to be that Friar is one step to becoming a Monk, which is untrue, they are two separate vocations in the Catholic Church. Monks live in self-sufficient, cloistered communities. Friars live, work, and minister among the people.
Further, the implication of being "just a Friar" is misused as justification for Carl's cursing toward the beginning of the film, and suggesting a sexual liaison later on. Friars are either ordained priests (think Robin Hood's Friar Tuck), ordained deacons, or they are vowed Brothers. None of these are "allowed" to curse (any more than any Christian), and all of these (except some Deacons) are celibate.
Carl says that the Battle of Masada was in "73 A.D." 'A.D.' is an abbreviation for the Latin 'Anno Domini' -- "In the Year of Our Lord". It is always written or spoken before the year mentioned (A.D.73 = In the Year of Our Lord 73).
'B.C.' is said after the date. 73 B.C. means '73 years Before Christ'.
In the opening scene in Paris, when Van Helsing picks up the wanted poster,the Eiffel tower is seen in the background only half built, however, when on the roof of the Cathedral, while Hyde is holding Van Helsing up, the tower can be seen fully built behind them.
After Dracula bites Dr. Frankenstein's neck, he pulls away with blood on his lips and trailing down his mouth. He wipes it away with his hand, but when he lowers the hand, there is clearly no blood on it.
When Van Helsing and Anna flee Frankenstein's castle, it's full moon. Their trip to Budapest then takes them better part of a month, since by the time they get there, it's only two days to the next full moon. And yet it only takes them a day to get back to Anna's home castle.
When Van Helsing fights Mr. Hyde in the second scene of the movie, Mr. Hyde steals his hat. Later, Van Helsing takes his hat back. Then, when he is thrown off of the roof, he loses his hat again. When Mr. Hyde falls and the police find him, they look up to the roof to see Van Helsing standing there, putting his hat back on. How did he get it back?
During the horse carriage chase sequence, Van Helsing is tearing through a narrow canyon with steep rock faces on both sides towering above the roof of the carriage. However, when Van Helsing is shown sitting on the coach-box from the side perspective, forest trees can be seen in the background instead of the rock faces.
When Anna and Velkan are fighting the werewolf at the beginning of the film, the werewolf chases Anna towards the cliff edge while Velkan is 'stuck' up a tree. How did Velkan get to the cliff edge to shoot the werewolf before it got there?
After the windmill collapses and Dracula and the brides land, in all the shots facing away from the windmill there are no villagers in the background even though there was at least a hundred of them seconds earlier with torches.
During the Brides' attack on the village, Van Helsing fires his crossbow at them many times, but the number of bolts (arrows) in its "magazine" never seems to decrease. When the crossbow jams, at least half of the bolts have suddenly disappeared.
When the brides hide from the sun in the village well, Anna slowly gets up. The camera angle shows behind her a few people hiding and a wooden bench. The scene cuts quickly to Van Helsing and back to Anna to reveal a dead body that wasn't on the bench before. As well the dead body's eye can be seen moving while closed.
At one point in the opening, Dr. Frankenstein is packing a trunk. When the scene cuts to the villagers and then back to Dracula and the Doctor, the trunk seems to disappear. It can in fact be briefly seen off to Dr. Frankenstein's left when he and Dracula are looking over the monster. Since it is implied that Dracula and the Doctor had a conversation between shots, they would have had time to move away from the trunk.
When Anna and Velkan are fighting the werewolf at the beginning of the movie, there are about a dozen people helping them. Who exactly are these people, and where do they disappear to for the rest of the movie, when Anna could have used more of their help?
When Velkan and Anna are trying to capture the werewolf, Velkan's gun is the only one that has silver bullets and thus the only weapon capable of killing it. Why didn't all the people involved have weapons with silver bullets in case something went wrong?
When the Cardinal and Van Helsing are walking into the lair for the Knights of the Holy order, if you look in the background you can see a reflection of Cardinal's robes, revealing an old film technique of using mirrors to make rooms look bigger.
When Van Helsing bends the metal bars blocking the way to the monster the bars are clearly made of some softer material. This is obvious since they start bending before the effort starts to show on Van Helsing's face.
The goof items below may give away important plot points.
In the final battle between Dracula and Van Helsing, when Van Helsing first begins turning into a werewolf, Dracula says (in a close-up of his face) "No! This cannot be!". During this close up, you can see a contact lens in his right eye.
At the end Anna's body is cremated. In the Middle Ages and Renaissance, cremation was forbidden by the Catholic Church. It was used as a punishment for heretics and unbelievers to deny them entry into heaven, and would not be an appropriate method to allow Anna to reach heaven. Carl would undoubtedly have known this and objected to any such ceremony.
Anna holds the syringe at shoulder height when she approaches the wolfed-out Van Helsing, and when he jumps into her you see her hand go over his shoulder. There is no way he he could have been stuck in his lower abdomen with the needle as the scene shows.
The weather and its effects in the Transylvanian village keep changing dramatically. When Van Helsing arrives in the morning, a thin layer of snow dusts the homes and ground. That evening, Velkan breaks into the Valerios home during a rainstorm that comes and goes, concealing and revealing the full moon. As Van Helsing chases him into the village, not only has the rain stopped, but it has started to snow again. The ground is again dry except for the snow, which at least should be melted slush after the rain. Then, after tracking Velkan to the nearby Frankenstein Castle, the rainstorm has started again.
When Anna encounters Aleera standing in the doorway, Aleera is wearing both earrings. When Aleera talks to Anna, her right earring is missing. But when Aleera slaps Anna across the face, both earrings are on.
When Frankenstein's monster swings down toward the bridge on the wire,
he gets caught on a statue on the side of the bridge, and dangle beneath the bridge. Carl pushes the statue off, allowing the monster to complete his swing, and he swings down, below the bridge, and crashes through a window, saving Anna. A few moments later, Anna grabs the same wire, and swings out the window. The window she swings out of is now far above the bridge the monster just swung beneath.
When Anna inspects the weapons room and finds her brother as a werewolf, it is clear that his shirt has already been ripped off of his body during his initial transformation, yet when he is human again, his shirt has reappeared to be ripped off during his next transformation.
When Aleera and Verona are about to kill Anna, Aleera says she wants the first bite and then she runs her empty hands through Anna's hair. In the next shot, Aleera tosses the glass (tomato juice.) over her shoulder. She obviously didn't have the glass in her hands the shot before.
When Van Helsing shoots Frankenstein's monster with the dart gun before he's placed in the graveyard, the dart gun is level, and looks like it should hit the monster's left-upper chest area, but in the next shot, the monster falls over with what looks like a dart in the left side of his forehead. Since the monster is much taller than Van Helsing, he would have had to hold the gun much higher to hit that location.
Just before the big final battle, Van Helsing stumbles around Dracula's laboratory. As two flaming Dwerger run out of camera view, you can see a cloud of carbon dioxide coming from an off-screen extinguisher to put the flames out (bottom right of the screen). The director and producer revealed this themselves on the DVD's audio commentary.
In the last scene Van Helsing looks out to sea and sees the sun low on the horizon, as if setting. Then when he is riding away from the sea he is riding towards the sunset. Since the battle with Dracula ended at midnight and it is the next day, the cremation would have been done in the early morning, with the riding scene taking place in the late afternoon. The supposed "ocean sunset" is obviously an "ocean sunrise".
When Dracula is front of the large mirror in the ballroom, none of the dancers' reflections can be seen because they are vampires. Previously, though, when the camera was pulling in on the dancers, we saw their reflections in a mirror on the left-hand side.
Despite having been heavily wounded, indeed loosing his arm, neither Mr. Hyde nor his alter ego Dr. Jekyll bleeds. Even if Hyde does not, for some strange reason, bleed, he should have done so when changed back into Jekyll.