Revealing mistake: When Sam is standing on the stairs with his hands up, just before Megatron grabs him and throws him onto the table for the 'Doctor', the rail and balusters in front of Sam have been set up to easily break for the stunt - note the short diagonal bits of wood propped up between them, precisely where they break for the grab.
Continuity mistake: When Sam rushes back to his dorm room, he paints the first symbol on the Bad Boys poster, then rips the top poster off the wall and paints large symbols on the wall in its place. That poster remains gone in all the following shots except for two, where it is back on the wall above the Bad Boys poster. First when Sam knocks over the microwave and then when Alice fully transforms on Sam's bed.
Continuity mistake: At the frat party, when Sam uses the cake frosting to write the symbols, in the first shot he writes the first symbol with perpendicular lines aligned with the cake's edge. In a following shot showing more frosting symbols, the original two lines have changed shape and position - none of the symbols are aligned with the cake's edge.
Continuity mistake: When Sam meets Leo in the dorm room, the bike near the window is not chained/padlocked to the metal bed frame springs. However, when Leo complains about Robo-Warrior the bike is chained/padlocked to the bed frame, but when Sam's parents walk in it's not again. Additionally, the bed frame moves from being in front of the window closer to the corner, to being directly in front of the window fan.
Continuity mistake: When Leo, Mikaela and Sam arrive at Simmons's deli in Brooklyn, note the clock hanging on the wall behind the counter. Between shots the time changes from 10:20 to 11:40 to 1:05.
Continuity mistake: In one scene we're shown a Predator B UAV taking off. This is a shot of an actual Predator B, which is a pusher turboprop. In a later scene we come back to the Predator, now on site, in a CG shot. The CG model is some kind of mutant Predator with a turbojet - no prop at all. This is the same mutant CG model used in TF1, but here it is a continuity error with the real shots.
Continuity mistake: During the shot where Mikaela runs into the lamp post, both the Pretender and the front bumper slide under the car as she backs up and drives forward again. Seconds later, as the camera angle changes and they drive away, the front bumper is re-attached with only a dent where it hit the post.
Visible crew/equipment: As Simmons and Leo are driving in Skids (the green Autobot) through the desert and Simmons says "One man betrayed by the country he loves" and Leo says "Stop saying that, oh my goodness, I'm in the car, you're not alone", there are two white screens visible in Simmons' glasses.