Revealing mistake: In the end fight scene between Viktor and the hybrid Michael, Viktor picks Michael up and throws him into a stone column. Terrible wirework then comes into play: Michael travels far too slowly towards the column for someone who was just thrown, he makes one perfect spin in the air on his way, and when he finally connects with the column, it's a delicate bounce off before the wire drops him on the ground. His legs don't even move from the "impact".
Revealing mistake: After Selene jumps off the building at the beginning and lands, there is a very large upwards pull (that stays in place until the camera cuts away) in her cape near her head that is in fact the drop wire running under her cape to the harness on her back (although the wire has been edited out).
Continuity mistake: When Lucian goes flying over Selene's car, in the overhead shot we see that the road below him has large parts with visible concrete because there are no paving stones. But in the next shot, a close-up of Lucian landing on his feet, the road is fully paved with paving stones.
Continuity mistake: At the shooting range, Selene is shown firing a black USP without a compensator. It then cuts to an over the shoulder shot, and she is now firing a two-tone USP Match (which she supposedly receives from Kahn to test out a few seconds later). It then cuts to a frontal shot of her, and she is once again using the same black USP. She never stopped firing, so she couldn't have switched guns.
Other mistake: When Selene's car plunges into the Danube, her car hit the bottom of the river on it's side (the passenger's side). When the camera closes up to the window of the car, you can see water flowing in from the roof of the car (as a result from the holes created by Lucian). It should flow (or at least accumulate) towards Michael's direction because of gravity but it did not.