Stupidity: After leaving the power plant to pursue the terrorists and retrieve the nuclear football, Jack orders the helicopter to take out the first Jeep. After he realises parts of the football are missing, why does he not order the helicopter to pursue and take out the other Jeep, preventing any further trouble from Marwan? (End of season 4's story, most likely).
Stupidity: When the couple is in the plant they call Jack on the cellphone, he instructs them to open the case and separate the book from the activation device. This was stupid, he should have told them to destroy it, since the codes had changed the moment Air Force One crashed, and it would take about 1 hour to make this work. This is explained later on in the show.