(at around 35 mins) In the first scene that General Custer is announcing his attack plans and asks if there's any questions, he tries to pronounce Sacajawea's name the first time, he is clearly standing on a crate above everyone else. The second time he tries, he is at the same level of everyone else. On his final attempt to pronounce her name, he's back on top of the crate.
(at around 9 mins) When Sacajawea is placed in her crate during the opening credits, she is lying in curly straw, with no white Styrofoam surrounding her. The lid is then put on the crate, however when she bursts out of the crate white Styrofoam is seen exploding out as she lifts the lid.
(at around 1h 3 mins) When Larry first arrives at the Air & Space Museum he sees the twin seat, twin canopy Air Force jet with both aircrew in the cockpits looking at him. Shortly after the aircraft is shown facing the other direction (no aircrew are in the jet) and one is walking on the ground below the aircraft. Not enough time passed for the aircrew to get out of the plane nor for Larry to change his visual perspective of the jet.
(at around 35 mins) When Custer is announcing his plan to attack when he yells "attack!" you can see Attila the Hun behind him in a corner of the crate. As he tried to pronounce Sacajewea's name, Attila is behind her. Then, as Custer sits back down, Attila is once again in the corner by Custer.
(at around 1h 2 mins) When Larry explains to Amelia why he left the job as a night guard, he places the tablet on a pillar near the Abraham Lincoln statue. When he is arguing with Lincoln, the tablet disappears, but then they leave and Larry is holding the tablet again without picking it up.
(at around 1h 10 mins) Larry and Amelia take off in the original 1903 Wright Flyer. This Flyer is only capable of carrying one person. Although they fly it using a stick control, it was actually controlled using a mechanism attached to the pilot's hips whereby he could turn the aircraft by shifting his body from side to side. Also, it no longer hangs from the ceiling of the National Air and Space Museum, but is in a second floor exhibit hall sitting on the floor.
The Smithsonian Institution does maintain storage for items not on display in the museums but they are located throughout the Washington D.C. suburbs, not in sub basements under the museums.
The Archives is not part of the Smithsonian Institution. It is also the National Archives, not the "Federal Archives."
(at around 1h 29 mins) When the giant octopus jumps into the reflecting pond in front of the Abraham Lincoln Memorial, it shows him jumping into a pool deep enough that he has to float up a bit to have most of his body above the surface. In fact, the pool is only 30 inches deep at the very center of the pool.
(at around 58 mins) The light on top of the Capitol is first shown as on when Larry and Amelia race to the Air & Space Museum. In later shots it is off. The light is supposed to be lit only on the rare occasion when the House or Senate are in session at night.
(at around 8 mins) Dr. McPhee has no reason to allow Larry to stay in the museum after closing, as Larry is no longer a night guard. However, Dr. McPhee may feel indebted to Larry after the events of Night at the Museum (2006), and decide to owe him this special favor from time to time.
Although George Armstrong Custer is typically portrayed with long hair and referred to as General, he had been reduced to his permanent rank of Captain after the Civil War. He was a Lieutenant Colonel at the time of his death at Little Big Horn - and had also cut his hair short to protect himself against being scalped. However, it's apparent that here he's portrayed in his Civil War "glory days" - he has a major general's shoulder boards and his double-breasted frock coat has the correct number of buttons. Additionally, he has his trademark red scarf and pin he wore on it at the time. Finally, he's portrayed as the 20-something he was 12 years before his death in Montana.
(at around 1h 27 mins) The first Night at the Museum (2006) established that if the tiles aren't perfectly flat on the tablet the magic didn't work. When Larry throws the tablet to Amelia, the tiles are obviously not flat but the magic of the tablet remains. When the tiles aren't aligned at sunset the magic won't occur. Once the magic takes effect the alignment of the tiles doesn't matter.
(at around 1h 6 mins) When talking about pi, the Albert Einstein bobble heads describe it as: "3.14159265, to be exact". Although the real Einstein would know that pi has infinite decimals, his bobble heads are giving the new combination to Ahkmenrah's Tablet, which is an exact number.
(at around 49 mins) When Jedediah is threatened with burial in sand, it is not the same threat as to a normal person. He is not a human who can suffocate but a toy figure who returns to life each night in presence of the tablet. However, some damage to him is certainly likely regardless of that fact, so the threat is still effective.
(at around 57 mins) Throughout Kahmunrah's conversation with Oscar the Grouch and Darth Vader, a Russian soldier is standing behind Ivan the Terrible's shoulder. However, when the camera flicks back to Kahmunrah as he waves goodbye to Oscar the Grouch and Darth Vader, not only has the soldier disappeared, but visible in the background is Al Capone whose skin is clearly not black and white as it should be.
If the tablet were truly made of gold Larry and Kahmunrah would not be handling it with just one hand or fingertips.
(at around 1h 10 mins) When the Wright Flyer is flying in the National Air and Space Museum, the timing chain is moving. While outside the chain has stopped moving, although the propellers are still turning. There is nothing in the plot to indicate that they ran out of gas.
(at around 21 mins) Brundon's security badge he has clipped on his belt has his picture on it but not his name.
Al Capone's Tommy gun is handled as if it were made of plastic.
(at around 1h 6 mins) The Egyptians did not have any concept of PI until over 800 years after the pyramids were built and when they did their calculation was (incorrectly) 3.16. The reason why PI seems to pop up in certain ratios of measurements of the pyramids is most likely because they could have used wheels as measuring devices.
(at around 17 mins) Larry tells his son that the Smithsonian Institution is a collection of 19 museums, which is true. However, he also says that they are all located on the National Mall. Some are actually located in New York City, Chantilly in Virginia, and different parts of Washington, D.C. The National Zoo is also part of the Smithsonian group of museums. The National Gallery of Art, though located among the Smithsonian, is not part of the Institution, contrary to the implication in the film.
The quick cuts between scenes in the Air and Space museum, the White House, and the Abraham Lincoln Memorial imply that they are adjacent. However the White House is 1 mile away and the Lincoln Memorial is over 1.6 miles away.
Grant Wood's "American Gothic" and Edward Hopper's "Nighthawks" are at the Art Institute of Chicago. Auguste Rodin's "The Thinker" is at the Musée Rodin in Paris. "Venus Italica" is at the North Carolina Museum of Art. Edgar Degas's ballerina is at the Royal Academy in London. Jeff Koons's "Balloon Dog (Red)" is not part of any museum's collection.
(at around 31 mins) When Larry opens up the octopus crate the octopus breaks out, which demolishes the crate, but not before. Later we see him break crates with just one of his tentacles but he couldn't break his own until Larry opened it.
Napoléon Bonaparte is depicted as speaking with a French accent. It is known that he never had one to speak of, always speaking French (a second language of his) with a Corsican accent, which sounds closer to an Italian accent.
George Armstrong Custer is portrayed with a southern (perhaps Virginian) accent, but he was from the Ohio-Michigan region. He introduces himself as "General Custer of the 7th U.S. Cavalry," but he was a general only in the 3rd Cavalry, and a lieutenant colonel in the 7th. Finally, the number of Federal soldiers who died at the Battle of Little Big Horn was 268, not a mere 208 as Custer claims.
(at around 1h 3 mins) The WWII Tuskegee airmen are wearing modern USAF flight jackets with Velcro. Although Velcro was invented in 1941, it was not patented and in common use until the 1950s. The same jacket has a 50-star flag patch, but there were not 50 states until 1959, 14 years after WWII ended.
(at around 1h 23 mins) Larry calls Able and Dexter "proud Capuchins." Although Dexter is a Capuchin monkey, Able is a Rhesus monkey. (However, Larry is not a monkey expert.)
(at around 42 mins) When Amelia tells Larry that he couldn't keep his "cheaters" off her "chassis" (her figure) she probably meant "peepers" off her "chassis" as cheaters was period slang for glasses and peepers was period slang for eyes.