Factual error: When the Autobots return to the moon in the present day to retrieve Sentinel Prime, they pass by the Apollo 11 lunar module (LEM). The LEM consists of an upper part (ascent stage) that houses the astronauts, and a lower part (decent stage) that holds the braking rocket used to land on the moon. When leaving the moon, the ascent stage blasts off, leaving just the decent stage on the moon. In the film, the entire LEM is shown sitting on the moon, which is impossible since the astronauts came back to earth.
Factual error: Many of the Washington, D.C., scenes show skyscrapers in the background, but there aren't any in D.C.
Factual error: After Sam and Seymour visited the Russian cosmonauts, they were attacked on the Interstate by three Decepticons disguised as dark SUVs. During this part of the movie, they are in the Washington DC area. However, during the chase, a green interstate sign is passed by and knocked down that is for I-88 to Aurora. This interstate is in the Chicago area.
Factual error: Several references are made to objects being on the dark side of the moon. The moon's rotation is locked into its orbit, meaning the same side of the moon always faces toward Earth. The dark side is simply the side facing away from Earth (which doesn't always make it dark since it receives sunlight when the moon is between Earth and the sun). For plot purposes, the Ark has to have landed on the dark side of the moon or else it would be visible using Earth telescopes because it is so big. But when we see Decepticons hidden on the dark side of the moon crawl out of the dust, Earth is floating in the background, which would be impossible since Earth is not visible from the dark side of the moon.
Factual error: In the opening scenes of the movie, set in 1961, the Very Large Array in New Mexico is shown. The Very Large Array did not exist in 1961, only being approved as a project by Congress in 1972, and being completed in 1980.
Factual error: While trapped in the toppling building, our heroes use bundles of computer cabling to keep themselves from sliding out. While bundles of cable are common around the US, they are against code in Chicago, which requires them to be in conduit in a plenum ceiling. Conduits would have easily prevented the bundles from crashing through an acoustic ceiling. And yes, that is a plenum building.
Factual error: Neil Armstrong's first step onto the moon as depicted in this film is incorrect. In real life he descended the LM ladder until he was standing on top of the little dish at the end of the landing leg. He then jumped back onto the ladder (the lower rung of which was a few feet up) to see if he could climb back up. He then jumped back down to the LM footpad. Then he stepped off into the dust to create the first footprint on the moon. The film shows him climbing down to the lower rung of the ladder, then just jumping into the dust where the initial footprint is immediately trampled by his movements.
Factual error: Big Joe has an AT-4 rocket launcher, which gets loaded before he wants to shoot the pillar. AT-4's are not reloadable.
Factual error: The ticker message received at "National Security Command" at the Pentagon at the beginning of Transformers: Dark of the Moon incorrectly lists a date of 7-10-62. John Kennedy is then shown giving his famous "Moon Speech" before Congress, setting a goal of sending a man to the moon and returning him safely to the earth. The only problem is that Kennedy made this speech on May 25, 1961. (00:02:45)
Factual error: In the beginning of the movie, the wrong year Lincoln Continental is shown. JFK was still alive and was assassinated in a presidential 1961 Lincoln Continental, but the one that pulls up to the white house is a 1965.
Factual error: When the NEST team is wing suit diving, the skyline of Chicago is reversed. Grant Park is to the south of the John Hancock Tower in real-life, and not to the north of it.
Factual error: Cybertron is placed between Earth and the Sun, as you can see in the shots from outer space. But it doesn't see to block the sunlight, despite being notably bigger than the Earth. It may be a framework but it's very dense with multiple layers.
Factual error: In the first scene inside the New Mexico VLA Radiofrequency Observatory, dated as 1961, the camera pans over to what looks like a high-definition radar display screen. High definition resolution did not exist in the 60s. (00:02:18)
Answer: Mudflap and Skids (the two idiot robots I believe you are talking about) were removed from the film due to negative fan reaction. While we don't hear what happened to them in the context of the plot, no reason not to assume they were killed in fighting between the movies. Arcee and Chromia (2 of the motocycles) were killed in the last film.