The first super computer that Rohit Mehra invents is visually different from the super computer that is reinvented based on the first one. Keyboard of first super computer rests on a metallic stand where as later one appears as it is simply floating in air. The first super computer is operated by left hand where as later super computer is operated by right hand.
At the circus, when the tanks explode, Priya's camera falls off her hand to the ground. However, during Krishna's wardrobe makeover, the camera is seen "conveniently" placed next to unconscious Priya's hand.
The computer that Rohit Mehra invents is coded with a password that is Rohit's retina and heartbeat. Scientists which could analyze his research to the extent that they completely rebuild the whole computer would realize how he encoded those in the computer, ultimately not needing those at all. Also, the new computer would not have those two things as code anyway; it would simply be without any code.
There is a time-line inaccuracy in last scene, when Dr. Arya shoots two bullets at Rohit and Priya, who are standing about 20 feet away. No human can change a pistol's target immediately after shooting one shot and trigger a second shot before the first bullet hits a target that is just 20 feet away.
Rohit is in Malaysia for two years working on a secret
project. At the end of the two years, his mother calls him up to say that his wife has given birth to a baby boy. Considering the fact that he was away from home for two years, where was his wife during this time?
Rohit is in Malaysia for two years working on a secret project. At the end of the second year his mother calls him up to say that his wife has given birth to a baby boy. He was away from home for two years so how did Hrithik impregnate his wife?
Some of Krishna's actions shown in the movie are impossible, like his climbing the mountain in a zigzag fashion, simply because of the protruding walls of the mountain which would come in his way. Another example is cracking a rock with a volleyball.