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 Sam and Jerry Wang are in the elevator, just after the other co-workers leave, Jerry takes a drink from his milk carton, placing the straw in his mouth, from the top of the straw, down to the hinge section. The shot cuts and there is suddenly less of the straw in his mouth. (00:40:00)
Continuity mistake: In the scene where Wang is pushed out the window by Laserbeak, when he lands you hear a car siren. In the shot prior of him falling, there are no cars on the ground below him. (00:43:40)
Continuity mistake: When the newscaster is introducing Simmons via his book, at first, he holds the book at the bottom, but in the shot directly afterwards, he holds it by the side. (00:54:15)
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: After Ironhide crashes into the remaining Dreads, we see that Crowbar lands on a bus stop, but when Sideswipe arrives, he is in front of an open garage door, at least 10 ft. away from the bus stop, debris is nowhere to be seen. (01:09:00)
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: After Optimus saves the day by shooting the Decepticon hovercraft, we get a small speech. When he says: ''For today, in the name of freedom'', his gun disappears. We never hear him throw it away, or see it lying around when Bumblebee transforms. (01:39:50)
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: When Sam is getting swung around by the decepticon, Lennox helps him and cuts the line. They fall past the height of the building (out of shot) then you seen Bumblebee coming to help them, and they're back above the building with the decepticon but in that time they would've hit the ground before Bumblebee could grab them. (01:58:00)
Continuity mistake: *Spoilers* After Optimus rips Megatron's head and spine out, he drops it right next to Megatron's dead body. But when Sam and Carly are reunited, the head with the axe lodged in it are much further away from Megatron. (02:23:00 - 02:24:35)
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: 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: 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.
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.