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.
Continuity mistake: In the first scene with Carly coming up the stairs she is wearing a white cap, when the camera changes to the front view and she is holding the stuffed rabbit the cap is gone. (01:01:30)
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.
Continuity mistake: When the Dreads knock over the freeway sign, the distance between the two green signs keeps varying.
Continuity mistake: During the chase with the black GMC's, Mirage has black rims in Ferrari mode. When they finish the chase, he now has chrome rims.
Continuity mistake: When Sam and Dylan are fighting, the clock behind them changes to different times every shot. It starts at 00:40, then 02:25, 00:15 and 11:00 in the following shots.
Continuity mistake: The shot of the Apollo 11 capsule approaching the moon is missing the lunar module, which is then seen attached to the craft in the next shot.
Continuity mistake: Towards the end of the movie with Chicago in ruins, the river alternates from green to brown through the entire battle.
Continuity mistake: When the guy in the back seat gets out of Epps' car, he is wearing a baseball cap and a Motley Crüe t-shirt. In the next shot, he is wearing full tactical gear - instantly. (01:37:15)
Continuity mistake: In the scene where Sam meets Dylan for the first time, the distance between Sam and Carly keeps changing.
Continuity mistake: *Spoiler* After Cybertron is pulled into Earth's orbit, they show that it can be seen from the earth's surface, pretty much the entire sky is taken up with Cybertron. However, in several scenes afterwards the sky is shown in the background as being crystal clear again.
Continuity mistake: In the scene where Sam, Carly and others slide down the collapsing building, the shot from above reveals only one window hole where they could have jumped from, and Sam and Carly are sliding quite far off to the side from the hole.
Continuity mistake: In the highway chase scene, one of the Decepticons knocks down the freeway sign which causes the signs, originally facing the on coming cars, to flip away from them. The other two Decpticons then use the signs to as a ramp to get further down the road. This should be impossible because the signs didn't land that way. When the Decepticons land, the signs are pointing the first way again.
Continuity mistake: Towards the end of the movie, when Dylan is pointing a gun at Sam, he has both hands on the gun. In shots of Sam, one of his hands is on his side.
Continuity mistake: Towards the end of the film Carly is holding Sam, in some shots she has dirty hands in front of his shoulders and in other shots she has clean hands that are over his shoulder.
Continuity mistake: In the NASA radio room, There are two men standing beside a cabinet. One a white shirt and tie, the other in a full suit. When the shot cuts, they have instantly switched sides, and the one who doesn't wear a jacket, suddenly is wearing glasses. (00:05:20)
Continuity mistake: When the Autobots return from their fake deaths, Optimus shoots down an enemy ship by destroying the right turbine, making it crash down and saving Sam. But later on, Bumblebee starts it up and flies it with no apparent damage.
Continuity mistake: When they all slide down the building, we get a shot that pans up. In this shot, Sam is the one closest to the bottom of the building and Carly is one of the people on the very top. Yet in the next shot, Sam catches up with Carly. (01:55:45)
Continuity mistake: Just before Optimus Prime arrives in the street where he kills ten Decepticons in twenty seconds, there is a shot of Sentinel saying "It's our world now!", and he is looking out over that same street. When Sam comes out of cover to take a look at Cybertron, Sentinel is still on the building. But when Sam shouts "Optimus!" Sentinel is gone.
Continuity mistake: In the scene when the characters are sliding down the glass building, just before they shoot the windows, there is a shot where a chair is sliding down along them on the left side. The camera dips down for a moment, and when it goes back up, the chair is gone, even though there is no hole in the building for it to go.
Answer: Mudflap and Skids (the two idiot robots I believe you are talking about) were removed from the film due to negative fan reaction. While we don't hear what happened to them in the context of the plot, no reason not to assume they were killed in fighting between the movies. Arcee and Chromia (2 of the motocycles) were killed in the last film.