Revealing mistake: When Kakihara is smoking in the beginning, you can tell the cigarette is not really lit, and that the glow of it was added later using computer graphics. The easiest way to notice this is to notice how no smoke is coming off of the cigarette itself.
Revealing mistake: When the one twin rips the man's arm off, the arm he is holding is not an entire arm, but more like 2/3 of an arm. It is ripped off slightly above the elbow. But in the next shot, you see the man is missing his entire arm almost up to the shoulder.
Revealing mistake: When Kakihara is attacked in the streets, protective padding is visible under his clothing. Look for it when he bends over backwards without falling over, before he removes his piercings.
Revealing mistake: After the girl has her nipples sliced off (in the uncut edition) in some of the shots where you see her dead body, you can tell her nipples are obviously still there, just being disguised (poorly) with makeup.