Plot hole: The puzzle box that Miles sends to his friends opens and closes on its own, but its hinges are not connected to any electromotors or kinetic mechanism.
Plot hole: This adaptation further exacerbates the problem of previous movie and TV versions; in the novel, Jackie would make the female designated witness talk over and over pretending also to get drunk after Linnet left to go to bed. In the Ustinov version it happened too, but the diversion didn't seem to last more than a couple minutes. Same in the Suchet version. Here, Simon even provokes Jackie practically the moment his wife exits the room. There's no time whatsoever for her to change and get in bed, let alone fall asleep.
Plot hole: During the shootout with Penguin and his gang at the warehouse Batman gets shot and falls to the ground. Penguin then creeps over to the spot he fell and realises he has disappeared and is in his car behind him. It is totally impossible for Batman to just disappear and get behind them without being seen, no matter the rain or firefight, that place was lighted enough and everybody was looking that way. (01:18:00 - 01:19:15)
Plot hole: Police Commissioner Clarke told arrestee Savage he could do 10 years hard time for armed robbery or "go inside Degnan [Correctional Institute] and get me what I want [evidence of civil rights violations]." Savage had not even been officially charged with any crime (s). A police commissioner does not determine what an arrestee will be convicted of or how much time will be served upon conviction. The Civil Rights Division of the Department of Justice investigates civil rights violations. (00:06:53)
Plot hole: When Cage and his wife and mates are going to the FBI safehouse the FBI agent shoots 2 baddies two separate times whilst Cage etc. are ascending the stairs, yet they don't hear the gunshots.