Plot hole: When the President of the United States attends a public gathering (such as the SuperBowl) the level of security is extremely high. So why wasn't Mason's delivery on the day of the game checked for explosive devices?
Plot hole: The bomb is found by Bedouin in the Golan (north of Israel). However, it was dropped in the Negev desert (south of Israel). How the bomb managed to move itself 500km is not clear. And Bedouin don't live in the Golan.
Plot hole: The Bedouin who found the unexploded nuke in the desert was supposedly dying of radiation poisoning when Clark questioned him. All he did was dig it out and load it in a truck, while all the shields were in place. If it was emitting THAT much radiation, the 3 scientists who spent DAYS refurbishing it for Dressler would have been made too sick by the radiation to finish the job.