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.
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.
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.
Continuity mistake: At NEST headquarters in Diego Garcia, when Galloway arrives holding up the Presidential order document, in the shot from behind him as he walks through the front gate, the booth is to his right (viewer's right) and the vehicle to his left (viewer's left), but in the shot facing him the booth is to his left (viewer's right) and the vehicle is to his right (viewer's left).
Continuity mistake: During the scene establishing the Decepticons on the Bayos freight ship, vehicles change. The first shot, overhead, shows Long Haul (green dump truck), MixMaster (grey cement truck), Rampage (red bulldozer), and Scrapper (yellow front loader with wheels). The next shot shows Rampage as being yellow, and Scrapper is now some yellow Volvo vehicle with treads and a claw. Also, by the angle of this shot and based on the previous shot, there would not be an angle to see through the background vehicles. In the next shot, when the transformers jump overboard, Rampage is red again, and the Volvo with treads is now the front loader Scrapper again.
Continuity mistake: When Sam is at the Frat party just after he has written the code on the table with cake, he goes and gets a drink. The glass is full, the camera cuts to the girl talking and then cuts back to Sam and the glass is nearly empty, cuts to the girl again and then back to Sam, with a full glass again.
Continuity mistake: In Sam's dorm room, there is a white mini fridge at the foot of his bed, flat against the wall under the Cloverfield poster. However, when Sam rushes after Mikaela just as Alice's 'tongue' grabs hold of his neck, that fridge has moved to in front of the closet door, but it moves back to its original position thereafter.
Continuity mistake: During the forest scene where Optimus Prime is engaged in a battle to the death, Sam is scrambling for safety. In some of the shots both of his hands are uninjured, but in other shots you can see that his left hand is bandaged/splinted. (This is a result of his "real life" injury in a car accident during filming.)
Continuity mistake: When the Cube sliver burns through the floor and falls onto the kitchen table, in the overhead shot there is a red stool on the side of the table (bottom of screen) with the bowl of cereal, but as the appliances transform that stool is at the wall beside the doorway. It reappears beside the table a few shots later, as the transformed blender jumps on it.
Continuity mistake: When Judy goes upstairs to pack after finding the baby booties, behind Ron there is a chair at the head of the dining room table, in front of the box he just taped. Then, just before Ron says, "Your mother and I are really proud of you," that chair has vanished, only to reappear when Judy shouts that she's crying again.
Continuity mistake: The multiple shots of the sinking Aircraft carrier are primarily shots of the CVN 74 (USS John C. Stennis) but also have shots of the CVN 72 (USS Abraham Lincoln) and the CVN 71 (USS Theodore Roosevelt). It is reported later on the news as the Roosevelt, and the Stennis is seen towards the end of the movie perfectly fine and providing air support.
Continuity mistake: When Sam is on the cell with Mikaela, telling her about the long distance relationship kit, he reaches for the webcam with his right hand outstretched while holding the cell with his left, but in the close-up it's his left hand picking it up, while holding the cell with his right hand.
Continuity mistake: After the Astronomy class, when Sam is in his dorm room he begins writing a green symbol on the Bad Boys poster, but when Leo and Alice show up that first green symbol has completely changed its shape and its position on the poster.
Continuity mistake: In the secret room below the deli's meat locker, when Wheelie explains that the symbols are the "language of the Primes", Sam picks up two photos, but both photos don't just switch hands as stated in another entry, one changes entirely. In the fist shot Sam holds a photo of a jet, but in the close-up he holds a photo of an old plane, then in the following shot it's back to the jet.
Continuity mistake: In the scene where Sam is on the phone and explaining his hallucinations in college, he drops his papers on the stairs and there is a man that passes him. When they change the shot, the man is behind him again walking from the top of the stairs.