Banned In Australia: According to this article, Australia's censors have banned the game due to the graphic violence in the fatalities. It's banned to such a point that they have the border patrol on the lookout for attempts to import the game. This could have been averted if they bit the bullet and introduced an R18+ for games, but that's a contentious issue.
It's also Banned In Germany. However, importing "banned" games isn't a big problem here.
Sheeva's ending in the game pokes fun at this controversy.
Following the introduction of an R18+ rating for video games in Australia in early 2013, the "Komplete Edition" has received approval and can legally be sold locally, as well as imported.
Executive Meddling: Kratos's different animations for when he falls victim to certain fatalities was a design decision which, according to Ed Boon, was requested by Sony Computer Entertainment as they didn't want to make him look weak.
"Portal Kombat": The release date of the game itself, simply for coinciding with that of Portal 2's; the temptation to switch out the "M" in "Mortal" for a "P" proved to be too great. And, considering that portals factor into the backstory so often...
Scorpion and Noob Saibot's second fatalities and the latter's Babality wouldn't seem too out of place in the Aperture Science Enrichment Center.
As usual, series co-creator Ed Boon moves his chords for Scorpion's iconic "Get over here!" and "Come here!" quotes (albeit thanks to re-used vocals from MK4 onward), as well as voicing a few minor background characters on the side.
Similarly, Raiden's gibberish yells during his Torpedo special moves are the exact same vocals from MK2 and Trilogy.
Seeing as Deception's Konquest mode established that Kenshi (the blindswordsman from Deadly Alliance and one of the few Ensemble Darkhorses from the post-MK3 era) had been around since the time of the first game (he had apparently Missed the Call for joining the tournament, and thus missed his chance to enact his revenge on Shang Tsung), many assumed that he had a good chance of making it onto the roster here. He was confirmed as DLC.
There had also been a fan theory since the time of Gold (thanks to Cyrax's ending) that the Lin Kuei's ranks do not consist exclusively of Chinese people (or those of Chinese ancestry in the case of the Chinese-American-Cyromancer Sub-Zero bros., who were taken to China against their will by their father). Smoke and Cyrax's bios confirm this to be true; the former hails from Prague and is named Tomas Vrbada, while the latter is Motswana and was recruited to join the clan (so... Slavic and African "ninjas"?).
Jossed: It had been assumed for years among the fandom that Jade's parents were Edenian nobility, thus explaining how she and Kitana were so close during their childhood and beyond. In reality, Jade was actually offered as a tribute to Shao Kahn in her infant years, where she was raised alongside Kitana as one of Kahn's assassins. It's unknown, however, if this is meant to apply to the original timeline, as MK9 has a few chronological deviations likely due to Raiden's actions, such as Mileena being created during the events of MKII instead of being created after Shao Kahn adopted Kitana and raised alongside her as Kitana's twin sister.