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: When Jessica Tandy walks into Mr. Faucet's house everything is in perfect shape except a couple of broken cups, and there's not a dead bird in sight. (00:59:40)
Plot hole: Reggie finds Tex's body stretched out on the bedroom floor, his feet tied to the radiator next to the wall and his hands bound to the bed frame, suffocated with a plastic bag over his head. The bed is a twin-sized, wood frame that Tex, a tall, strong young man, could have pulled the end of it with his hands and arms close enough to his face to at least attempt to tear a hole in the plastic bag so he could breath. He was obviously conscious early on because he wrote the name "Dyle" in the dusty floor with his finger. Considering the floor is covered in dust, there's not even the slightest sign of a struggle to free himself. Instead he just neatly prints the name on the floor before he dies.