The scene with the Friar in the lab is an homage to all the James Bond movies with 007 and Q's lab. Hugh Jackman (Van Helsing) is rumored to be chosen as the next Bond after Pierce Brosnan. See more...
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Continuity: When Velkan hangs on the rope and is being pulled up he looks down and the werewolf climbs up the wooden pole and you can see scratch marks on the top of the pole. Then the second time he looks down at the werewolf you can see the top of the pole is scratch free and the werewolf makes the scratch marks again. If you have a close look at these two scenes you can see it's the same scene played twice, but with a different roaring sound from the werewolf.
Continuity: Towards the end of the movie, in the scene where Anna is taking the werewolf cure to Van Helsing and the vampire bride stops her on the large fallen pillar, she falls so she is in a sitting position with the cure in her left hand. She then switches it to her right. Then in the close-up shot, the cure is still in her left hand and she switches it again.
Continuity: When Dracula and Van Helsing meet for the first time, Dracula's hand placement changes between shots. This happens twice, once when he is saying 'But like me, hunted by all others." During this, his hands move from his side to taking his gloves off. And again, when he says 'You are the great Van Helsing,' his hands move from his sides to being in the air.
Factual error: In the beginning of the scene after Van Helsing kills off one of the three female vampires, there is a map behind Friar Carl depicting the whole of the Carpathian basin, which, at the time, included the Austro-Hungarian empire as well as a part of Romania. However, the whole area is labeled "Transylvania", which is only a region of Romania.
Revealing: At the end of the movie, when Dracula's children explode, the goop from their bodies doesn't match up with the splashes on the ground. You can see some of it hit the ground and disappear, and other places, it would hit, then the splash would occur a second or two later. It was all computer-generated, so it was just slightly mismatched. Hard to catch normally, but easy to see in slow-motion.