During the train sequence, the train is first shown crossing Bandra station. Then it is mentioned that the train crosses Vile Parle (Parla) station. Finally it crashes into the CST Station, which is actually in the opposite direction to the direction of travel shown earlier.
In the train sequence, the train travels from Bandra to CST. This is the harbor line route of the Mumbai locals. None of these harbor line trains have 12 coaches, while the train in the movie had 12 coaches.
According to the plot, Ra.one cannot kill G.one and vice-verse until both have their H.A.R.T plugged into their system.The only way to kill either of them is with the Anti-H.A.R.T gun (with only one bullet) which appears at level 3. Nowhere in the film is it mentioned what would happen if both Ra.one and G.one misfire the bullets.
In the song "Criminal", the girl wearing the panty has "Crimnal" written on it, without an "i". Later in the song, on the same girl's panty, the mistake is corrected & now the panty has "Criminal" written on it, with an "i".