Plot hole: Simmons stands outside the 'The Monastery' at Petra (not to be confused with 'The Al Kazneh' at Petra where Indiana Jones and the Last Crusade was filmed) and looks at the horizon, and he is able to see the Air Force landing with Optimus by the pyramids. It then appears to take them mere minutes to drive over there. This is outright laughable, even accepting that they make the trip in an alien robot car. Petra and Cairo are separated by hundreds of miles of desert, not to mention Israel being between Egypt and Jordan.
Plot hole: In the beginning of the film the Fallen is nearly barely able to live. Jetfire explains that without Energon, Transformers will "oxidize and rust, like my wretched self!". But after Optimus dies, the Fallen is suddenly able to do serious combat. Where did he get that new energy from, when The Matrix of Leadership is said to be the only remaining source of Energon?