Continuity mistake: At the end of National Treasure 1, Riley has a Ferrari 360 Spider. At the beginning of Book of Secrets, when his car is being towed away, it's a Ferrari F430 Spider. At the end of the movie, he is given back a 360 Spider.
Factual error: After Ben kidnaps the President he calls and tells Riley to meet him at the Library of Congress in ten minutes. Traveling from Mount Vernon to the Library of Congress in ten minutes is NOT possible. Even in the middle of the night with no traffic it would take a MINIMUM of 30 minutes to make that trip.
Factual error: While the group was in the gold cave, Riley helps himself to one of the gold bricks, which is larger than a "standard" gold brick, and is roughly three inches thick, eight inches wide, and about twelve inches long. A brick of gold this size would weigh around 250 pounds, which would make it nearly impossible for Riley to carry around, even in a backpack. Even if it were ten carat gold in the brick, it would still weigh over 100 pounds.
Continuity mistake: When Ben Gates and company first examine the Booth diary page, they notice a few of the digraphs relevant to the cipher. After he says to flip the page, pause it and notice the digraphs that are visible. They are: ME IK QO CQ TE ZX. Later, when Ben discovers that the key to decoding the cipher is DEATH, Riley inputs the keyword into his computer. Pause it when it shows his computer screen. The various digraphs that they have input are nowhere close to the ones they discovered on the page. They are: QF JU WJ AK EH. Not even the same amount of digraphs, no less. The results are larger too. The entire interface is different for the two shots.
Audio problem: In the final scene of the movie, when Riley is walking toward his car, he walks approx 30 feet from behind the car up to the car, notice that there are no other cars behind him. As soon as he starts the car he accidentally goes in reverse and we hear him crash into another car, yet there was no one behind him for at least 30 feet. We did not see or hear another car pull in behind him in that few seconds. There is no car parked behind him.
Factual error: In the scene where Ben and Abigail are using the service lift to get to a different floor in Buckingham Palace, Ben presses the button on the exterior, then shuts the door. This is inaccurate as, with that type of lift, pressing the buttons when the doors are open does nothing. The lift can only move if the doors are closed when the buttons are pressed.
Continuity mistake: Mitch Wilkinson jumps to a hanging ladder in the hidden chamber at Mount Rushmore, the first shot shows him hanging off the ladder with a pistol holster through his belt loops. The shot cuts away and when it returns there is no pistol holster where there was seconds earlier.
Revealing mistake: In the scenes where Riley is using his computer to look up information on the "SearchInfo" site, the screenshot used is of Wikipedia. (You can even see the "About Wikipedia" link on the left).
Revealing mistake: In the scene where the barrels of beer are rolling off the truck, you can notice small squibs going off to make the barrels look like they have been shot.
Factual error: When the group comes to Mount Rushmore, they arrive at a lake. There is no lake close to Mount Rushmore (look at Google Maps, the lake used is Sylvan Lake, which is a good 15 miles away from Mount Rushmore). Mount Rushmore is suppose to be a "cover up" for the final treasure and that would make the chamber underneath the faces itself.
Plot hole: When the characters are trying to escape Cibola through the central drain, the drain is actually, as Ben and Patrick imply, really just a room which dead ends, and they have to open the door to keep it from filling up. If this were the case, the entire city of Cibola and the room above (where Ben first says that all the water goes out somewhere) would have been completely filled up with water over the centuries. But in the movie the water had apparently been draining through that central "drain."
Continuity mistake: When Ben and Abigail are examining the Resolute desk at Buckingham Palace, Ben starts opening the drawers and discovers the code option numbers on the underside of the drawers for the first time. When he does this, in the shots of the underside of the drawer, Ben is pulling the drawers out almost all the way, but in the shots from above, he is barely pulling the drawers out at all.