One major plot hole in this film is the choice of location for the final battle. When you are a group of outmatched light infantry with inbound air support against giant mecha, it is generally not a good idea to go into a city where said giant mecha have protection from air attack due to being surrounded by buildings such that the aircraft have a hard time hitting them. It also has the glorious effect of putting all of the civilians in danger . Interestingly this is a plot hole that is somewhat corrected in the second two movies. In Revenge of the Fallen they fight in a dessert and show what air power can do to giant exposed targets. And in Dark of the Moon at least they have the excuse that the Human's weren't running towards the city, the Decepticons chose the location.
One minor plot hole is that Epps initially says that F-22s would never fly between buildings and so a single aircraft doing so must be Starscream. Later during the ending scene in which the F-22s attack Megatron they do so by flying between buildings to launch their missiles.