Factual error: The ticker message received at "National Security Command" at the Pentagon at the beginning of Transformers: Dark of the Moon incorrectly lists a date of 7-10-62. John Kennedy is then shown giving his famous "Moon Speech" before Congress, setting a goal of sending a man to the moon and returning him safely to the earth. The only problem is that Kennedy made this speech on May 25, 1961. (00:02:45)
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)
Revealing mistake: Toward the end, when Sam is going to destroy the tower he gets kicked in the stomach by Dylan. When Sam falls he lands on another part of the destroyed building, you see the chunk of building that he lands on conforms to his body, showing that it is made of foam to soften his landing.
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.
Factual error: In the beginning of the movie, the wrong year Lincoln Continental is shown. JFK was still alive and was assassinated in a presidential 1961 Lincoln Continental, but the one that pulls up to the white house is a 1965.
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.
Continuity mistake: When Charlotte Mearing, the United States Director of National Intelligence is talking to Optimus Prime about the teleportation device, the position of her hands on the red hand rail differs between shots.
Continuity mistake: After Ironhide crashes into the two remaining Dreads, both of them transform. We get a close-up of one of them, who transforms over a lamppost, about 10 feet above it. The next shot has him past the lamppost, and at the same height as the lantern itself - instantly.
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: When Optimus takes the roll to avoid getting shot by Shockwave, you can see the very distinct clock of the Hotchkiss building can be seen in the background, yet they aren't fighting in front of that. In the next shots, the building in front of which Optimus rips out Shockwave's eye is much more modern.
Continuity mistake: During the freeway chase, there is a shot with Hatchet landing on a car on the opposite side of the freeway. This shot has all sorts of poles on the center guardrail, and structures in the background. Then the poles in the center disappear, and the white-ish buildings in the background change into a bridge.
Continuity mistake: When Optimus takes a dive after his rampage in front of Shockwave, you can see that it is actually in front of the building with the control pillar in it (note the very distinct clock in the background) yet when Optimus shoots the dome and the pillar down, he's a good distance away from it.
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 NEST is tracking The Dreads, in the satellite shot there is hardly any traffic on the freeway. However, in the shot immediately afterwards, it's very busy.
Continuity mistake: When the Autobots return to base to protect Sentinel Prime, when they enter you see Sideswipe after Sentinel Prime, but when they are in you see Ironhide after Sentinel Prime instead.
Continuity mistake: When Carly nearly reaches Megatron, there is a slow-motion shot of her with an SUV blowing up in the background. In the first shot, it flies up in an upright position. In the second shot, it suddenly spinning.
Factual error: When the NEST team is wing suit diving, the skyline of Chicago is reversed. Grant Park is to the south of the John Hancock Tower in real-life, and not to the north of it.
Revealing mistake: During the highway scene with the black GMC Decepticons chasing the Autobots, a number of civilian cars are flipped. If you look at the underside of a few of the cars, you can see the hole they use to launch a post to help flip the vehicle for the stunt. A brief puff of white smoke can also be seen on a Toyota Camry which is from the CO2 used to launch the post during the flip.
Audio problem: In the Russian bar scene the female bartender cycles a pump action shotgun at Dutch when she is holding a double barrel shotgun. Dutch then disarms her, when he turns the shotgun back on her you can hear a pump action shotgun being functioned and an empty shell hitting the floor. Dutch is holding a double barrel shotgun in the scene.
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.