Mudlfap, along with Skids, are not shown in the Dark of the Moon film because they were described racist stereotype's. Michael Bay defended the two Autobots and described them as "good, clean fun" and said that the Autobot twins "put more personality in the film", but they were cut from the movie in response. Although all the scenes with the two twins were cut out of the movie, there is one scene were they are shown. When the Autobots are driving into NEST headquarters, the twins are shown at the very end of the line of Autobots. Later, what appears to be Mudflap can be seen parked next to Sideswipe, when Sam comes to NEST for the first time.
Although they are not intentionally shown in the movie, they are shown in the movie adaption. Into site http://www.tfw2005.com/boards/transformers-movie-discussion/480983-getting-rendered-deleted-scenes-4.html, you can find two deleted scenes on the movie with Skids and Mudflap.
Mudflap is present when the Autobots are awaiting Colonel Lennox and Director Mearing, and he is apparently talking to Wheeljack alongside Skids. They are also present outside of the base when Ironhide, Ratchet, him, and Skids await the arrival of Sentinel Prime, Mirage, Bumblebee, Sideswipe, and Sam Witwicky. However, Sentinel betrays the Autobots upon his arrival, and executed Ironhide with his Acid Rust Blaster. As Bumblebee is about to be executed - Skids takes the aim and is killed. Mudflap tries to avenge his fallen brother by attacking Sentinel in anger, but Sentinel shoots Mudflap, which causes him to rust and fall apart as well, and die.
Mudflap also appears in the film's novel, and is first seen arguing with Skids. He and Skids are also present outside of the base with Lennox, Ironhide, and several NEST soldiers, as they await the return of Sentinel Prime. However, when Sentinel betrays the Autobots upon his arrival, he executes Ironhide with his Acid Rust Blaster. As Bumblebee is about to be executed by Sentinel as well - Skids takes the aim, and his legs begin to rust, and his head falls off his shoulders. Mudflap tries to avenge his fallen brother by attacking Sentinel in anger, but Sentinel fatally shoots Mudflap in the mouth, which causes him to ultimately rust and crumble apart.
Optimus, while speaking to the President, recieves a message from Ratchet that Ironhide, Mudflap, and Skids have been killed by Sentinel. Optimus doesn't believe him - but looks into the situation, and concludes that as for Mudflap, "his mind is a frenzy. He is fighting Sentinel, but is really dead and doesn't realize it yet."