It is stated in scene in the apartment and reinforced in the helicopter scene following the failed attempt at Extraction that Saito was in-effect interviewing Cobb for the attempt at Inception, and that initially Saito thought that Cobb had failed the interview until he realized that they had put him in a two layer dream.
It is implied that he had therefore deliberately allowed himself to have the attempt at Extraction made on him and that he was prepared - by being mentally prepared he did not seem to store too many important secrets in the safe, and that he was suspicious of their approach to sell themselves as anti-extractors.
Later in the movie, they use the 'Mr Charles' gambit and deliberately make Fischer aware that he is in a dream. Perhaps the gambit they use against Saito where they pretend to be friendly Extractors pitching to train a wealthy individual to defend against extraction work well against a mark who is not expecting it. Against Saito, who is prepared and has allowed himself to be introduced into a shared dream, maybe it is an approach that makes him become aware that he might be dreaming.
This is also the scene where we are introduced to Mal, she speaks to Cobb as he begins his attempt to break into the safe, and then enters the room with Saito and Arthur at gunpoint. Together with her subsequent appearance in shared dreams with Ariadne, this begins to suggest that Cobb's subconscious projection of Mal is directly working against him - perhaps that she directly warned Saito.