The guy who gets his car stolen by Ed Harris in London is the same guy who got his Hummer stolen by Sir Sean Connery in The Rock (1996), another of Jerry Bruckheimer's movies which also starred Nicolas Cage and Ed Harris.
When showing the map of the grounds to the President, Ben tells him it belonged to a slave of Washington's named Charlotte. This is the same name as in the clue to the Templar treasure that Charles Carroll gave to Gates' ancestor (and which turned out to be the name of a ship). Presumably Mt. Vernon was one of many dead ends which Ben pursued in his search for Charlotte and the Templar treasure prior to the events of the first movie, which would explain why he knew about the hidden compartment and how it worked, or it might just be a sly reference to the first National Treasure (2004).
Disney discovered that the shooting schedule at Mount Rushmore would displace the local Hill City High School prom that is held annually at the location. To make up for this, Disney paid for the prom by providing transportation to a new location in Rapid City, door prizes at the prom, and scholarships for the valedictorians.
Patrick Gates (Jon Voight) lives in the same house used in Father of the Bride (1991), Father of the Bride Part II (1995), and Mr. & Mrs. Smith (2005). Jon Voight's daughter Angelina Jolie starred in Mr. & Mrs. Smith (2005).
The night before the scenes at the University of Maryland were to be filmed, a half inch of snow fell. The crew then had to use fire hoses to hose down the entire McKeldin Mall and nearby locations to melt the snow for continuity in the movie.
In the Booth diary, the remaining part of the page after the words "Thomas Gates Artifex" (artifex: Latin, nominative singular, a noun meaning "master") is the latinised Greek word "Aenigmatum", (genitive plural) meaning "of puzzles". The Latin word and Greek word brought together mean "master of puzzles".
According to the website Ten Facts About the Mansion-Mount Vernon, Mount Vernon has a full basement, but there are no secret passages leading from it. The Mansion basement or cellar played a key role in this movie, and although there is no tunnel leading from it, it was an extremely important part of life in the Mansion. The cellar was used for a variety of purposes, and was divided into several rooms. One room, closest to the kitchen, has a large fireplace, and was used as a dining area for the housekeeper and other white servants, as well as to heat food before it was served to the Washingtons. When Washington died in 1799, there were a variety of items stored in the basement including wine, sand for rustication, and potatoes.
In the second scene with Agent Sadusky (Harvey Keitel) and his two Agents, Agent Sadusky can be seen wearing crossed U.S. and Marine Corps flags on his lapel. Keitel is a former Marine. He wore them in the first movie as well.
While examining the lost page of the diary, the "historians" say that John Wilkes Booth studied Latin because of the writing in the diary and the fact that he said, "sic semper tyrannis", after shooting President Lincoln. Real historians (or screenwriters) should know that J.W. Booth along with his brother and father were famous actors and their best known performance was of Shakespeare's Julius Caesar. In that play the character of Brutus yells, "sic semper tyrannis" just before the famous slaying in the Senate. John Wilkes always wanted to play Brutus, but his father never let him, instead picking his brother Edwin for the role. It seems that John Wilkes did eventually get to say those famous lines on stage.
When Ben and Abigail visit the White House, Ben gets into a confrontation with a small boy. When the boy goes to leave, he can be seen curling the index finger on his left hand. In another Disney movie, The Kid (2000), with Bruce Willis, this finger curl is a trait of the young Russ Duritz, played by Spencer Breslin. This movie was also directed by Jon Turteltaub, and the finger curl is a sign of annoyance.
In the car chase scene in London, the stunt driver for Nicolas Cage's car was Top Gear (2002)'s The Stig (Ben Collins) according to his autobiography "The Man in the White Suit: The Stig, Le Mans, the Fast Lane and Me".
The saying made by John Wilkes Booth after his assassination of Lincoln, and leap from the balcony, "sic semper tyrannis" is a shortened version of the Latin phrase "sic semper evello mortem tyrannis", meaning "thus always bring death to tyrants".
This was Jerry Bruckheimer's second film and the second Disney film to feature a significant portion shot at Universal Studios, the caged exhibits in Cat People (1982) we're filmed there and the town of Genovia in The Princess Diaries 2: Royal Engagement (2004) was filmed in the Little Europe set.
The trivia items below may give away important plot points.
The script originally called for Mitch Wilkinson (Ed Harris) to stab Patrick Gates (Jon Voight) in the scene where they escape from the flooding gold city. This was taken out in post-production, because it made the character "cross a line" that Director Jon Turteltaub felt ought not be crossed. This is why there are almost no shots of Patrick Gates remaining in this scene. He was bleeding, and that's hard to hide. His sweater in the next scene had been ripped from the stabbing, and they were able to "unrip" his shirt with CG.
The area of the Library of Congress, in which Gates finds the Book of Secrets, does not exist as an area of book shelves. These book shelves were constructed as a prop library in a previously empty balcony of the Library's Main Reading Room, and dismantled after the scenes were shot.
The Ferrari, which gets impounded in the first few minutes of the film, is a Ferrari F430 Spider. However, at the end of the film, he is seen in a different car, the Ferrari 360 Spider, which is the same model he drove at the end of the first movie.
It shouldn't come as a surprise that Thomas Gates would be associated with the Confederacy. In National Treasure (2004), Patrick Gates displayed in his library a portrait of Confederate General Thomas Jonathan "Stonewall" Jackson.