Revealing mistake: During the Ukraine scene when the man is being shot down by Laserbeak in his Car, his wing goes through a tree.
Revealing mistake: A Decepticon ship crashes into and destroys a fair amount of the Tribune Tower's steeple. Later, a wide shot of the city shows the Tribune Tower with white blocks composited on top of it. The animators forgot to put the damage into this shot.
Continuity mistake: When Crowbar dropped his weapons in the ''Mexican stand-off'' we get a look at his ''dread locks''. When he pulls the spike which he throws at Ironhide, the locks disappear, only to return in the subsequent shots.
Continuity mistake: In the first scene, as Carly comes up the stairs, it is bright and sunny outside. As Carly leaves, it is raining, but when Sam walks outside and sees his parents, it's bright and sunny again.
Continuity mistake: In the scene where Sam and Carly are trying to get into the Autobot base, Carly is wearing a black jacket, after Sam sees Bumblebee, she is wearing a brown one, and inside she has a black one on again.
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)
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.