John Henry Irons aka Steel (Man of Iron) has an appearance in the film hitting an Atlantean with a sledgehammer during the final battle scene in Metropolis. This is a slight nod towards the true storyline of how Steel originated by being saved by Superman while attempting to help out in a fight against Doomsday.
This animated film is based off the "Throne of Atlantis" storyline which was a 2013 comic book crossover event between the Justice League and Aquaman series in the New 52.
While this film's events takes place after La Ligue des justiciers : Guerre (2014), in the comics there is a five year gap as the events of Justice League's six issue origin story take place five years ago when superheroes were first emerging (around the same timeline as the Superman Action Comics), while the seventh issue of the series moved the timeline to the present (where most of the other New 52 series take place).
While both Shazam and Green Lantern are seen as part of the Justice League in the film, in the comics they were not present. This is because in the comics the Justice League had not met Shazam yet, and Green Lantern had quit the League because of the events of the previous storyline "The Villains Journey" had led him to believe that his attitude had endangered their mission and quit in order to protect the League's reputation. Additionally The Flash was the only active Justice League member not involved in this storyline in the comics as it was mentioned he was defending Central City from Gorilla Grodd and his army (which refers to the "Gorilla Warfare" storyline that takes place in his own comic book series).
In the film Cyborg immediately agrees to have his remaining lung replaced with cybernetic lungs to allow him to survive underwater. In the comics, he initially hesitates believing he would sacrifice more of his humanity, but following the League's capture by Atlantis, agrees to undergo the operation in order to save them.