Plot hole: Roger's initial briefing at the beginning of the film states that 'Tom' goes out from 104 and 'Harry' from 105. Despite this the goons are said to be in 105 when they find the entrance to Tom.
Plot hole: Bond lies to Tanya on the date the embassy would be bombed (Karim and Bond knew the 13th) and Tanya denoted the deception by telling Bond when he came in the decoding room she thought it was the 14th. How did Grant know to A: be on the train and B: have an entire escape plan set up for the wrong day?
Plot hole: In the beginning of the movie, all of the cars turn to the left to head south. However, the map at the police station indicates that they had to turn to the right to go south.