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? (00:12:30)
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. (00:47:05)
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. (00:52:00)
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. (00:50:35 - 00:51:30)
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. (00:54:05 - 00:55:05)
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. (00:11:20)
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. (01:22:35)
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. (00:53:50)
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. (00:55:35)
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.) (01:00:05)
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. (00:34:15)
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. (00:54:00 - 00:54:55)
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: When Alice and Leo walk in on Sam in the symbol filled dorm room, on the wall at the head of Sam's bed are three small-to-medium sized framed photos of Sam and Mikaela hanging vertically. After Alice pushes Leo out of the room, the frames change. Now there are two large and medium frames hanging vertically and another medium frame hanging horizontally. (00:50:00)
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.