When Viktor pulls the pendant from his daughter, the cord which
it hung on breaks nearly completely off leaving only about 1 or 2 inches on either side. When Lucian snatches it off the dusty floor before leaping through the window, the entire cord is intact.
Towards the end, Selene frees Michael from the examination table by shooting off the chains attached to the handcuffs that bind him to the table. In the next few shots, when Michael is yanking off the ropes that had been around his chest, the handcuffs themselves have disappeared from his wrists, including the chains.
The shooting gallery scene: in close-ups of the statue targets, bullets are slamming into them at a high rate, as if from a machine gun. When the shot changes to show Selene, she is actually seen to be using a semi-automatic pistol, and firing at a much slower rate.
Selene throws four throwing-stars at the Lycan "Raze" in the sewers, in the sequence where they are removed one shot is mirrored so that the last star jumps from left to right shoulder and then back again for the final ripout.
A bald man wearing a green jacket and carrying a blue backpack appears to board the subway train three times during the opening sequence. We see him in front of Michael standing next to the subway train doors; then we see him walking past Raze toward the train; and then a second later we see him walk past Raze toward the train exactly as before.
During the assault on the Lycan base, as Den Kahn and his men are cautiously clearing out a tunnel, Kahn is clearly holding his rifle with his right hand on the pistol grip and left hand on the fore-grip. When we see him peer down a dark tunnel, all close-ups of the rifle and tunnel show his hands being reversed with left hand on the pistol grip and right hand on the fore-grip.
When Selene is practising shooting into the statue head, she is using a H&K USP Pistol. This switches to the H&K USP Match pistol for a few shots, then back to the first USP Pistol. Then the slide locks back like it's empty and there's a quick edit and she keeps firing until she finally runs out and the slide locks back again.
The Beretta 93 series is chambered for the 9mm Parabellum and
a double-stack magazine can hold 21 cartridges. In the hallway scene, Selene nearly empties both magazines. Yet, without obviously reloading or reasonable time to do so, Selene empties the equivalent of another magazine from each gun into the floor.
Silver nitrate is a clear substance and looks nothing like the quick-silvery fluid seen in the movie, even in high concentrations (though it may turn black if stored for long periods). This may have been done intentionally however.
The bullets shown in the close-ups have little glass "windows" on the shell casings, and show the UV liquid or liquid silver nitrate inside. If this were a real bullet, there would be no room in the shell for gunpowder. A shell casing is ejected from an automatic weapon, not actually part of the slug/projectile as depicted in the movie.
Viktor is referred to as 'The oldest and strongest vampire', but if Marcus Corvinus is the first vampire, and is an elder still living in the current time in the movie, then Viktor cannot possibly be the oldest.
Lucian, despite having the variables to prolong his life via Raze's delivery of Amelia's blood, dies needlessly. It is revealed that Viktor and Amelia's blood in combination with Michael's blood could produce a uber strong hybrid. Raze even drops the blood before Lucian in the holster. Previously, Lucian injected himself with Michael's blood to complete 1/2 steps. Only needing Amelia's blood to fulfill his goal. Yet, he does not.
When Selene is telling Kraven that she thought Michael was important to the Lycens Kraven says, "Lucien wouldn't be the slightest bit interested in a human," but Lucien is supposed to be dead, killed by Kraven - Selene should have found that odd at least.
At the beginning of the battle between Viktor and Michael, Viktor hurls Michael across the water and into a pillar. As soon as the camera changes to show Michael getting up you can clearly see the cord used to pull Michael across the room on the ground leading up to his back.
Just before the werewolf with stars in him (thrown at him by Selene) gets them removed, he walks in holding someone's body over his shoulder. He is supposed to be naked because of the transformation, but you can see a small pair of black underwear.
When Kahn rolls the grenade down a shaft full of Lycans, the grenade bounces out of the puddle at the bottom. As it does this the explosion begins from within the puddle, underneath the still airborne grenade.
When Micheal is thrown backwards into a pillar, while fighting Viktor, the rest of the action is normal, while it appears to be that Micheal is moving in slow motion. Obvious to the fact that he is being dragged into the pillar, and not very hard.
The goof items below may give away important plot points.
Incorrectly regarded as goofs
We know that Vampires and Lycans can transfer memories to those they bite. For example, Selene gives her memories to Viktor and Lucian gives his to Michael. But in that case Selene would have already known that Viktor was responsible for the death of her family, because he turned her into a vampire. However, Selene's memories in Viktor's head were garbled, because she couldn't transfer them well enough. Obviously, just being bitten isn't enough to transfer memories - a complicated and conscious effort is required as well. Viktor even says that only elders know how to do it properly. Certainly he would know better than to transfer the self-incriminating memories to Selene, which explains why she doesn't have them.