Other mistake: When you play the DLC side mission "Wonderland," notice all three missing cop cars have the same license tag.
Continuity mistake: When you find Gordon in the mall he's wearing his jacket. When you rescue him just after your final fight with The Arkham Knight he's not. Then he's got it back later at the asylum.
Batman: I am vengeance. I am the night. I am Batman.
Trivia: When Batman enters the clock tower, there's a flashback scene of Barbara being shot by the Joker. Before this occurs, go to the back wall and zoom in on the movie poster, "Dark Interlude." One of the names on the poster is Matthew Hagen. In "Batman: The Animated Series", Matthew Hagen was an actor who was transformed into the shape shifting villain Clayface.
Question: How could Batman be infected if he cured himself of the Joker's poisoned blood in Arkham City?
Answer: He was exposed to the fear toxin when it was unleashed on Gotham City.
How does that explain him being still being infected? The four people he had at Panessa studios were infected by a blood transfusion but Batman cured himself of his. Plus, the fear toxin only makes a person see their worst fear.
Answer: He was infected through a blood transfusion.
The Joker infected Batman with a blood infusion in Arkham City but Batman cured himself so, it would make no sense for him to still be infected.
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Answer: He was exposed to a toxin bomb, so he probably got a bigger dose of the fear toxin.
The fear toxin only makes a person see their worst fear. It doesn't make them physically transform into it.