How does John figure that Sir Galahad is a "castle" rather than a "knight" - both seem equally likely. But identifying the "piece" as a knight would have yielded a totally different result.
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.
It's a common mistake in many TV shows, but when Stella and John talk at the end, Stella's glasses have totally flat lens - they'd be useless for improving vision. The actress doesn't wear glasses in real life, but they have her wear them here to make her more brainy-looking. But they make them flat lenses so they don't interfere with her vision.
(talking about sewers)
Digger: It's a great way to get around. I should know, I worked down there in my youth. Three years as a sandhog. Burrow through rock so the rest of you can enjoy the little things – electricity, running water, dial tone.
Frank: So that's why they call you Digger?
John: Are you a digital or analog kind of girl?
Stella: Oh... whatever gets the circuits going.
Mourner: Hi. Long time, no screw with.
Music: "Lapdance" - N.E.R.D.
John Walsh is credited but they just reused the tape from his earlier appearance.