When inspector Arjun Dev runs for Sanjay Singhania for the first time when Sanjay is in the bus. The inspector successfully enters the bus even after running for it, as the driver of the bus could stop it. When he gets in, Sanjay Singhania is missing. If he could have got off the bus, the inspector could have seen him, but he didn't - so where did he go?
Gia Khan has never seen Asin, but when they were looking for the archives of newspaper to complete the story of Amir Khan she spotted the news paper correctly with Asin's photograph. How could she identify someone's picture when she had never seen her?
In an earlier scene, we see that the police officer found Sanjay's diaries and then a scuffle ensued leaving the place in disarray. When Sunita went to Sanjay's apartment shortly after, the police officer now bound and gagged in a cabinet, we see Sunita opening a drawer and finds the two diaries inside a drawer.
At the near end of the movie, when Sanjay is following Ghajini on Bike, the SUV in which Ghajini is going is a 2004 model Land Cruiser. In the next scene a 2008 model Land Cruiser is seen. Again in the next scene it becomes a 2004 Model
Sanjay Singhania (Aamir Khan) suffers from Anterograde Amnesia, whereby a person remembers everything before the incident which caused the problem. Therefore, he should have remembered his personal assistant as well as the flat which he bought for Kalpana (and later used as his base). However, he relies on photographs and notes to remember these things as well.
Sunita (Jia Khan) goes to library and gets a newspaper from archives department and takes it to the school, but in reality libraries never gives old newspapers to take home. And in the newspaper you can see girl's picture clearly printed on the front page but in reality you never find any such photographs without their face covered.
It is shown that Sanjay reads the content of his diary in the hospital, with additional help from Sunitha. But it is practically impossible to know what happened in the past two years within 15 minutes. And adding to that, Sanjay shouts madly after knowing the "flashbacks" of his life, though he shouldn't be remembering anything.