John Doe

John says the first victim was a limo driver. However, when we saw the scene originally Lt. Avery said there were other victims and she hoped the limo driver's death wasn't related to those. In fact, when John puts together the clues at the end, the first two murders prior to the limo driver's aren't mentioned even though they would presumably confirm John's hypothesis and give further indicators as to what specific game was being recreated.

When John and the police work on the puzzle they start with 5-6 people working on it simultaneously. But later, with time ticking down, only John and Lt. Avery are working on it. Couldn't they find a few more cops to help solve the puzzle and stop the building from blowing up?

When he arrives at the strip joint John says that Pescoe said that ATF stands for "All Time Favorite." Ummm, not that we ever saw or heard. Pescoe had the whole conversation about Sir Galahad's, then the police hustled him away so there was no chance for any other conversation.