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.
Revealing mistake: When Clayface disguised as Joker is holding Talia hostage in the movie theater, they are both standing on stage in front of the screen with a movie playing. However, they are not casting shadows on the screen. Also, no shadow appears on the screen when Clayface takes on his true form.
Trivia: Just before Protocol 10 starts, you end up in a giant fight with Joker and a good number of his goons. If you activate Detective Vision during this fight, you'll see that Joker doesn't have a skeleton. This is also true when he's holding Talia hostage in front of the move theater. This offers a hint to how the plot plays out.
Trivia: In addition to Black Mask, there are two other cameos in the game's intro sequence. When you're making your way through the prison line, one of the prisoners says to Bruce, "You're on my list," and pretends to shoot him with his finger. This is Deadshot, who would later appear in one of the game's side missions. A little bit later, after you go through the armored door, look up at the roof of the building towards the right. You can see Azrael, who disappears in a puff of smoke. Again, he later appears in one of the game's side missions.
Mr. Freeze: You will bring me Nora or you will die.