Continuity mistake: When Sam is in his bedroom, after he finds the Cube sliver it falls and dramatically burns a hole through the floor into the kitchen. But Sam's bedroom is over the living room (there is nothing on the ground floor below Sam's elevated bathroom, and in the first movie Jazz hides in this open space), and the kitchen is actually located between the den and dining room, at the other end of the house. If they were to follow the actual floor plan of the house, the Cube sliver would have landed in the area of the piano in the living room, but where would the fun have been in that?
Continuity mistake: While Mikaela and Sam are on the phone with each other (after the failed webchat date the night before), when Wheelie starts reaching up for the safe's combination lock in the first shot, there are no mouse traps on the floor near the short stool to his left, nor are there any cigar boxes. However, in the next shot two mouse traps (a snap trap with cheese bait and a glue trap) and two cigar boxes have all suddenly appeared. Wheelie proceeds to step on the two traps and then stands on the two boxes to reach the combination lock.
Continuity mistake: After Mikaela throws the metal box at Alice and breaks the window, when Sam runs out of his dorm room screaming we see (and have seen multiple times prior to this) the wall and bathroom door opposite his door. Oddly enough, in the next shot from the hallway, Sam, Mikaela and Leo are actually leaving from a door that's farther down the hallway. Sam's actual door is the first one on the right, opposite the bathroom door - there is a bike wheel leaning against the wall beside the bathroom door.
Plot hole: Simmons stands outside the 'The Monastery' at Petra (not to be confused with 'The Al Kazneh' at Petra where Indiana Jones and the Last Crusade was filmed) and looks at the horizon, and he is able to see the Air Force landing with Optimus by the pyramids. It then appears to take them mere minutes to drive over there. This is outright laughable, even accepting that they make the trip in an alien robot car. Petra and Cairo are separated by hundreds of miles of desert, not to mention Israel being between Egypt and Jordan.
Continuity mistake: The Saturn that Mikaela is driving has a moonroof that encompasses most of the roof, over the front and back seats. When the Decepticon Grindor captures them, in the interior shot looking up at Leo as Grindor seizes the Saturn, the car has a solid roof over Leo, which is also seen in the interior shot as they fall.
Factual error: The team go to the Smithsonian Air and Space Museum's Stephen F. Udvar-Hazy Center, which is located adjacent to Dulles Airport in Virginia - surrounded by rolling green hills - to find a Transformer. When Jetfire breaks out of the museum, beyond the broken door is a large, desert airplane graveyard with large mountains in the background. This appears to be the 309th Aerospace Maintenance and Regeneration Group (309 AMARG), a well known aircraft 'boneyard', located at Davis-Monthan AFB, in Arizona.
Visible crew/equipment: When Ron and Sam are discussing college and girls, in the shot facing Mikaela, as she's airbrushing the design on the motorcycle, the reflection of a crewmember (wearing a blue shirt) holding a reflector screen is visible on the chrome surface at the left, and as the camera pans in closer to her its moving shadow is also visible.
Continuity mistake: When the Saturn has been dropped by Grindor, as the car falls with Mikaela, Sam and Leo inside, just before they crash land in the last interior shot, Mikaela's and Sam's headrests have vanished, and a large sticker has also suddenly appeared on Sam's visor in this shot. The headrests reappear when they are upside down.
Continuity mistake: When Lennox is demoted his rank is ripped from his shirt, but when he turns around his rank is back where it was originally.
Continuity mistake: At the Smithsonian Air and Space Museum, when Mikaela, Sam and Simmons follow Wheelie they reach Jetfire's enclosure with the large information plaque attached to the metal front bar, as Wheelie faces them. Next shot, that whole front horizontal bar is gone along with the information plaque, and Wheelie now faces Jetfire. Then when the Cube shard attaches itself to Jetfire the metal horizontal bar reappears, though the large plaque is still gone, and that bar vanishes once again in the shot from under Jetfire.
Continuity mistake: Mikaela is wearing high heels when she reaches the stairs, before entering the library. Then in the library, her high heels have vanished and she is suddenly wearing flat shoes in this scene.
Continuity mistake: When Mikaela, Sam and Leo get into the Saturn there are no headrests on Sam's and Mikaela's seats, but when they kill the Pretender and are driving away, the headrests are suddenly there.
Continuity mistake: When Mikaela phones Sam and says that she's breaking up with him, in the first shot of Sam as he walks down the hallway toward his room there is no curtain in front of the window to the right, but in the second shot as he reaches his room, there are white curtains draped over the windows. Then, when Sam runs into the hallway because of the fire, the curtains are gone again. In fact, the white curtains are actually outside the window - someone had closed the windows over the curtains. The curtains reappear again when he runs back into his room with the extinguisher.
Factual error: In the scene where Galloway parachutes out of a C-17, Major Lennox asks Galloway if he is "familiar with the standard MC-4" parachute as he is helping Galloway don said parachute. The parachute that actually deploys when Galloway pulls the ripcord is not an MC-4, as MC-4 parachutes have rectangular canopies (shown correctly later in the film as the NEST team descends into the desert).
Visible crew/equipment: After Bumblebee has blown up Sam's bathroom and Sam orders him to get in the garage, as Judy shouts, "Holy mother!" the reflections of the moving boom mic and two crewmembers (one wearing blue short sleeves and the other wearing white short sleeves) are visible in the window to the right.