Plot hole: Several: 1. How did Hush get Batman's fingerprints on the knife? 2. How can the likes of Mad Hatter, Zsasz, and Deadshot go through the prison city without being spotted? 3. Why wouldn't Batman suspect Ra's al Ghul being the power behind Strange once he discovered him in the prison city?
Plot hole: The side mission "Fragile Alliance" has Batman helping Bane destroying containers full of Titan. After destroying the containers and returning to Bane, a small fight ensues followed by a cut scene of Batman trapping Bane. Bane has the drug Venom visibly going through his body the whole time so he could easily break out, but remains trapped through the rest of the game.