Continuity mistake: Mr Freeze's ship just appears out of the clear blue rather than having been anchored all night when you can play "In from the Cold."
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.
More questions & answers from Batman: Arkham Knight
Answer: In Batman: Arkham City, Mr. Freeze's gun was taken by the Penguin, which he used in an attempt to stop Batman. After beating the Penguin and the eventual closing of Arkham City, the gun was then sent to the GCPD evidence room.
But Mr Freeze got it back for his fight with Batman, remember?
Rob245