Factual error: A person with 60% burns on his body would not be wearing pyjamas, as the Hungarian guy does. (00:19:45)
Factual error: When the Suspects planned to kill Kobayashi, they waited for him in the office building. McManus got into the elevator and waited for the three men, hidden in the roof. After Kobayashi and the two men got into the elevator, and the lights went out, McManus fired twice. The blood on the wall behind Kobayashi would be correct if the two shots came from in front of the men. But McManus fired from the roof of the elevator, meaning the blood spray should be much lower on the wall and angled sharply downward. (01:05:50)
Factual error: When the burnt Hungarian guy is interrogated the first time a doctor insists that everyone wears masks (even though Jack Baer is very lax about it). When he is surrounded by doctors the second time none of them bothers about masks. (00:38:10 - 01:01:40)
Answer: Keaton doesn't believe in Keyser Soze, and is so convinced that Kobayashi is the one pulling the strings and manipulating them. They figure that if they take HIM out, they are home free.