There is a scene where a tv in the background is discussing strange activity on mars. This is a reference to the introduction of the Martian Manhunter.
This is the first appearance of Batwing (Luke Fox) in media outside of the comic book medium.
When Jim Gordon is giving a speech about Batman's disappearance, the news channel on the bottom right says "News 52". It is a reference to the new 52 line of DC Comics.
The film is based on the comics Batman: Battle for the Cowl and Batman: Incorporated.
This is Jason O'Mara's 5th time voicing Batman in an animated film.