Minor Plot hole: In a shocking twist, it is revealed that the Russian President was not killed but simply poisoned by Salt. The information is however revealed days later. Did the doctors decide to keep their mouth shut? What about the press? What about the Russians? You think they would be concerned to know as soon as possible if their President is dead or not.
Minor Plot hole: After Salt attempts to kill the Russian President, she is (1) handcuffed with her hands in front of her torso, (2) with handcuffs that let her move around her arms almost freely, (3) put inside a special police car with no separation between the driver and back seats, (4) and with a police officer sitting right next to her on the prisoner's seat. Any of those 4 points are completely impossible. But she got all of them.
Major Plot hole: In the final scene of the movie, Salt has to flee from the U.S government and the CIA because no one can believe her that she actually saved the President and stopped the Nukes. But what about the President ? He was there. He saw Ted Winter kill all his staff and threaten him, surely he could say that Salt was not responsible.
Major Plot hole: Because Ted Winter doubted, with reason, that Salt could potentially turn against Russia, he convinced Orlov to blow her cover inside the CIA headquarters. There is however two big problems with this plan. First, it reveals part of the whole secret operation to the CIA; one of the only organizations that can stop them. Orlov does not only expose Salt; he also exposes the time and place of the assassination plot against the Russian President (which is crucial to their plan).
He could simply have said anything else, or nothing at all. Second, his plan assumed pure luck in order to succeed. To be successful, both Orlov and Salt had to escape from the CIA headquarters. How could he be so sure that everyone would be lucky enough to escape dozens of trained and armed Swat members? Because the script told him.