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CTU recovered Yosik Khatami's cellphone (the terrorist meeting with Prado) which Khatami used to contact Marwan just before meeting Prado. Curtis mentions on site that they'll try to pull information from it but we never see CTU make any effort to do so. All the scenes following has Jack and CTU focusing on Prado and his knowledge on Marwan's whereabouts, which could equally be traced from passive triangulation of Marwan's cell, a method used on numerous occasions previously.

Mike Novick says that most of the nation is asleep, however in the previous episode he said that most of the nation is wide awake.

In the closeup camera angles of Yosik Khatami (the terrorist meeting with Prado) at the marina, it is raining but in the long shots it isn't.

When Jack leaves Prado's interrogation room to talk to the lawyer, he just opens then door; there is no keypad to enter a code. However there is one on the other side of the door. Shouldn't it be the other way around to prevent suspects from just escaping the room?

Prado is a mercenary, with no apparent loyalty to Marwan's cause, and therefore is presumably looking out only for himself; yet CTU never even tries to make a deal with him, offering immunity/protection in exchange for his information. They just jump right to torturing him.

Marwan reads off the missile coordinates as "Latitude 37 degrees, 14 minutes, longitude 115 degrees, 21 minutes." That would be southern Nevada, but his henchman punches them in and brings up Jefferson City, Iowa. Not only that, but there is no Jefferson City, Iowa. There is a Jefferson, Iowa (in Central Iowa), as well as Jefferson County, Iowa (in Southeast Iowa).

Mike Novick describes the area in eastern Iowa where the warhead was hijacked (most likely just west of the Quad Cities) as "mountainous terrain." There are no mountains in Iowa.

How could "Amnesty Global" possibly decide to take on a case, assign lawyers, find a judge still awake, and get a court order complete with a US Marshal to enforce it, within half an hour; and all this after midnight?