Other mistake: When Sam and the others are in the building, and then sliding down the side of it, the angle at which the building is compared to the ground seems to change many times. The angle, rather than simply increasing gradually, goes from very large (when we first see the Decepticons firing at its base) to very small (when we focus back on the team inside the building and the chairs are only just starting to roll across the room, indication that the building is barely slanted) and then back and forth between large and small depending on the angle of the shot when they are sliding down the side (and this is not just an impression due to the angle of the camera). When they then break through a window and come back into the building, the angle of the slant is again too small. (01:53:45 - 01:56:30)
Other mistake: So let me get this straight: Optimus Prime has Energon Swords hidden in both of his arms, with which he can slice through an entire Decepticon in one chop, yet when he is hanging from a few wires, despite having one arm entirely free, he can't cut himself loose?
Other mistake: In the scene with Richard Nixon speaking to the Apollo astronauts, the TV showing the phone call shows a lamp behind his head, and the seat being right behind him. But if you look at the actor sat there, there is no lamp, and the angle of the camera shows the chair would not be in shot.
Other mistake: In the scene where Laserbeak picks up Sam and drops him off the building, Sam smashes through a glass wall with a handrail. Earlier on, he climbs over this handrail. No way would he have the momentum to smash a metal bar.
Other mistake: When the Autobots return during the fight they say they were hidden in the first booster rocket to break off. When their rocket exploded the first boost rocket hadn't broken off yet.
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.