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.
While this film's events takes place after Justice League: War (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 scene where Superman and Wonder Woman are eating at a diner as Clark and Diana, the blonde girl at the table next to them is the character model of the Wonder Girl (Wonder Woman's Protégé) Cassie Sandsmark from the now cancelled Young Justice animated series (who was the second Wonder Girl in the comics). There is also a nod to this as Lois says to Clark "It's a wonder women date you".
In the original comics, Cyborg is forced to call in reinforcements to deal with the Atlantean army in the form of Black Canary, Vixen, Firestorm, Element Woman, Black Lightning, Gold Rush, Hawkman, Zatanna, and Green Arrow (who was the only one that did not respond). In the film this is omitted.
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.
The trivia items below may give away important plot points.
In the post credit scene, Lex Luthor approaches Ocean Master and offers him a spot on his new team. This is a reference to the Injustice League, a team comprised of supervillains similar to the Legion of Doom.
In the film it was revealed that Orm was the one behind the attack (who was being manipulated by Black Manta) with the nuclear missiles on Atlantis in order to frame the surface world for the attack. In the original comic book storyline Orm was not complicit in the attack and it was revealed that Aquaman's advisor Nuidis Vulko was responsible for the attack to manipulate Orm to start an attack hoping to goad Arthur to take up the throne of Atlantis afterwards (and also allow for Vulko to end his exile from Atlantis), something that does come to pass when Arthur reluctantly agrees to prevent a similar tragedy, but not before both Vulko and Orm are arrested for their crimes. Vulko's role was cut from the film, with Black Manta taking his place of manipulating Orm's actions instead, with Black Manta's goal of plotting to steal all of the treasures of Atlantis for himself.