Continuity mistake: Carly's shoes appear to mysteriously alternate several times between black stiletto heels and black ballet flats in-between shots during the climactic action sequence. This is most noticeable during the collapsing building sequence as well as the scene in which Carly speaks to Megatron.
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.
Continuity mistake: When Sam is first shown at his new flat and the two small robots appear, Sam has a small argument with them, and takes one of the robots in his hand to put him on the floor, but in between these two shots Carly walks in front of the camera thus focusing our attention on her, but if you look at Sam putting the robot down, there is nothing in his hand. And when it's only him in the shot again the robot comes back. They must have missed adding the CGI maybe because he was in the background of the shot at the time.
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.
Plot hole: When we see Sentinel Prime being extracted from the Ark by Optimus, we can see that Sentinel Prime already looks the same way as he does throughout the rest of the movie. The Ark crash landed in the 1960's, the Rosenbauer Panther Fire Truck didn't exist in the form we see Sentinel Prime transform into. All of the other Autobots came to Earth in their proto forms and adopted a disguise when they arrived [we see them scanning alternate modes - one Decepticon is shown doing likewise in this movie.]. Sentinel Prime already has his disguise when on the ark, which isn't possible.
Continuity mistake: In the scene with Richard Nixon speaking to the Apollo astronauts, the TV showing the phone call shows a lamp behind his head, and the seat being right behind him. But if you look at the actor sat there, there is no lamp, and the angle of the camera shows the chair would not be in shot.