When the Cobra is knocked down the first time, the back of his pants is wet, as if he has sat down on something wet. 30 seconds later, the first wet spot is gone and he instead has two new spots on the back of his legs.
When Sean is following the kidnappers with his mentor on to the roof, just when he reaches the bricked windowed house, you can see the kidnappers and the mentor waiting for their cue to get through the door.
During on of Chan Lee's fights on board the ship, her double's face is clearly seen.
The kids at the start watching the match have obviously been badly dubbed over with adults putting on high voices.
General Andreas is obviously dubbed by another actor, and there is glaring lip-flap between his mouth and the voice dubbing him when he speaks.
The entire plot of the movie relies on the villains kidnapping Sam and injecting him with a virus. They picked Sam due to his combative abilities early in the film. There is no reason to go through all the trouble they went through to get Sam, the tricks with disguising as his master, sending ninjas to attack him, when they could have just stuck upon him unawares, especially when all it took was to shock him with their weapon to paralyze him. They could have snuck upon him when he was sleeping, or at anytime during the fights with this weapon to incapacitate him. This would have been especially useful when his friends had no idea where he was during the initial chase scene at the warehouse.
The head bad guys in this movie must really hire and train some incompetent thugs. In one scene in a slum alley, one of the good guys, Dexter, easily defeats a supposedly "professional" ninja. This is unlikely, since it would require years of special, intense training to do so, and it is never revealed that Dexter ever had such training.