Plot hole: When we see Sentinel Prime being extracted from the Ark by Optimus, we can see that Sentinel Prime already looks the same way as he does throughout the rest of the movie. The Ark crash landed in the 1960's, the Rosenbauer Panther Fire Truck didn't exist in the form we see Sentinel Prime transform into. All of the other Autobots came to Earth in their proto forms and adopted a disguise when they arrived [we see them scanning alternate modes - one Decepticon is shown doing likewise in this movie.]. Sentinel Prime already has his disguise when on the ark, which isn't possible.
Plot hole: The film tries to claim that all six lunar missions were to collect samples from the Ark. However, the missions had landing coordinates hundreds of miles apart. If only 35 people knew about the secret mission, that leaves hundreds of thousands of others who believed they were working toward actual lunar exploration, meaning it would be very difficult to fake telemetry data without someone noticing. Also, there are long range photographs of the different landing sites showing the landing craft at their true lunar landing spots.
Plot hole: In the scene where Sam and Carly are attempting to communicate to the military through the UAV drone, Sam tells them all about the Decepticons' plan to bring Cybertron into our atmosphere. But Sam was never there when Dylan explained the plan to Carly, and there was no time for Carly to have told him.