I tried to make the title as specific as possible without being a spoiler.
In the movie,
Khan demands that Spock return the torpedoes. Spock reassures Khan that "Vulcans cannot lie. They are your torpedoes," and clearly omits the key detail that the bodies had been removed from the torpedoes.
Why didn't the villain, with his super intelligence, see through this, when the entire audience could?
Everything in here is a spoiler so I added spoiler tags
The entire audience has access to the information that Spock has spoken to Prime Spock and as such would know what Khan did not.
To wit
Prime Spock reveals that Khan was the most dangerous, most ruthless and most brilliant opponent he and his Enterprise ever faced and that they won only at great cost. Without this interaction, it is unlikely Spock could have won, because as he so fond of saying "Vulcans never lie."
In addition
Khan, being arrogant, would never consider a Vulcan capable of breaking his word. He never considered that Spock, being half Vulcan and having such a capable teacher as James T. Kirk, would ever do anything that would amount to such an unpredictable lapse of behavior.
Also.
Every interaction Khan has made with the Federation since his attacks had gone according to plan. He never considered he might find a match in intellect and in Spock's rage, an opponent capable of being physically his equal. This is Khan's failing, an inevitable over-estimation of his ability with an undervaluing of anyone else's.
I think it is a question of perspectives. We calm and safe and with no vested interest in the fictional situation have the luxury of being able to carefully analyze the dialog for loaded phrases as well as knowing (because it is a film) that somehow the Enterprise will win and Spock is likely to defeat Khan in a battle of wits and somehow in a physical match too (due to the line "what use are you for breaking bones" earlier in the film). Khan was heavily vested in the situation, emotionally and physically drained with no idea that Spock might be clever enough to subtly trick him with a turn of phrase. He considered the Enterprise helpless and his victory certain - so far everything seemed to have pointed towards him being several steps ahead of everyone, including Spock. Do not forget how arrogant Khan is and how far beneath him he considers everyone.
In the original film they trick Khan in a similar way by using the prefix code to lower the Reliant's shields under the guise of sending information about Gensis. Khan knew about the prefix code (when his shields dropped he realised that the Enterprise had lowered his shields and shouted "The override, where's the override") but in the heat of the moment it simply did not occur to him that his opponent might be smart enough to still find a way to fight.
When Spock spoke to the Old Spock of the future he asked him if he knew who Khan was and when he found out he did he ask the old Spock how he was defeated. The old Spock started out by saying he made a vow not to reveal anything that would change his destiny, then he said "That being said" and started to tell Spock about Khan. Since the old Spock was familiar with Khan's characteristics which would include his weaknesses, he was able to explain to young Spock that Khan was easily decieved by using simple measures. I assume since Khan is such an arrogant and complex individual, simple ideas went undetected by him. He would have explained how they tricked Khan. In the Wrath of Khan they tricked him by using a simple code on the radio "Hours would seem like days" and so on. By using another simple form of deception they were able to defeat Khan again. Basically using the concept that it worked once it should work again.
