Marcus' attempt to use a super ship to start a war with the Klingon Empire recalls something Weller's character in Star Trek: Enterprise, John Frederick Paxton, said. In both cases Weller takes an extreme "Us versus Them" mentality.
Beam Me Up, Scotty!: Subverted and inverted. You wouldn't think Scotty himself would make this request.
JJ Abrams and the film's writers said they didn't feel comfortable tackling an updated version of Khan. They lied. Likewise, Benedict Cumberbatch swore up and down that his character in the movie was original; and until his character was officially named John Harrison, the entire cast vehemently denied he was playing Khan whenever they were asked about it.
Leonard Nimoy said he had nothing to do with this film. He lied, as he got a cameo.
One of Us: In a rather hilarious contrast to Robau's stern nature, Faran Tahir has been known to openly nerd out in interviews about how cool it is to play a Star Trek captain.
Reality Subtext: The central plot, involving Admiral Marcus and his plan to turn Starfleet into a more militaristic version of itself, is largely a reflection of the fandom's response to the 2009 revival; though it revitalized the Star Trek franchise for a new generation, quite a few longtime fans criticized it for emphasizing action and conflict at the expense of creative storytelling, and for trying to take a famously optimistic franchise in a Darker and Edgier direction. Fittingly, the final battle pits the Enterprise against the Vengeance, the first Starfleet ship ever designed expressly for combat, and the ending has Kirk delivering a speech about the importance of Starfleet staying true to its original mission of peacekeeping and exploration.
The designs and whatnot for the Klingons were originally created for scenes cut out of the 2009 film.
Chris Pine recites the "Space, the final frontier" monologue before the end credits. For the 2009 film, Abrams considered having Chris Pine recite the monologue before letting Leonard Nimoy do it as a Passing the Torch moment.
Some fans were no doubt rolling their eyes when Abrams seems to setup a monster chase scene early in the film. The creature is instantly stunned and never seen again. Adding to the humour, it turned out that the monster was actually Kirk's ride, intended to help him escape from the horde of angry tribals pursuing him.
Ironic in that Star Trek II: The Wrath of Khan was originally planned to be entitled Star Trek II: Vengeance of Khan, because at the time the third "Star Wars" movie was announced to be 'Revenge of the Jedi.
Carol Marcus was supposed to be American like her original counterpart but was changed to English when Alice Eve was cast.