Continuity mistake: When the girl is tied up in the room, Haru shoots the big spear-like arrow through the room. When the machine that it's attached to comes through wall, it knocks the bomb off of the table it was sitting on. But, by the time the machine makes it through the other wall into the warehouse the bomb is neatly on the machine and removed from the room that the girl was in.
Plot hole: Wouldn't the bomb (when in the back of the truck of the bad guy driving away) vaporize him, considering he wasn't that much far apart than Allison was when she was tied up? He is even quoting as "Are you comfortable? Well it doesn't matter considering you'll be vaporized before you know it," when she was about 4 ft away.
Continuity mistake: The red Chrysler Convertible used in the movie changes. In the "normal" scenes it's the model built in the middle of the nineties, when they shoot at it it's an older one (without a facelift).
Revealing mistake: When Haru looks through the phone-book, you can see they took a real phone-book and simply glued a strip of paper that had 10 rows of fake names and numbers over a section of it (leaving space to make "Tanley, Martin" stand out). You can also see the name are briefly out of alphabetical order because of this. (And anything seen that is not covered by the strip of paper is a real person's actual address and phone number).
Continuity mistake: When Gobe parks the car by the counterfeiting warehouse near the ending, it's parallel with the warehouse's wall. When Haru gets out of the car, the front is pointed toward the wall. Then when Haru is climbing up the palm tree, you can see that the car is further away from the warehouse than it was before.
Continuity mistake: In one scene Hauru's "brother" is talking with the master ninja about Hauru. The brother has a gold necklace around his neck, but in the story line he does not receive that necklace until later in the movie.