In celebration of the one-year anniversary of its mobile release, the iOS version of Injustice: Gods Among Us received a major free update that added multiplayer and a slew of other features. It's an outstanding update on paper, but unfortunately it appears the update isn't behaving nicely for quite a few users. My friend texted me earlier today: "Very pissed. Injustice reset my acct for some reason. Lost everything." Upon further research, it appears he's not alone, with most of the iTunes reviews and Facebook posts now mentioning the lost game data.
While it doesn't appear that Warner Bros. Interactive Entertainment (WBIE) has addressed the issue directly, I did find a "Basic iOS and iCloud Troubleshooting" page on the studio's Online Support site, which may help. The steps after the first image is what you may want to try if you fall victim, where it discusses restoring an old iCloud save. Sadly, that solution doesn't seem to work for everybody though.
In addition to the data wipe, it seems that the update brought some "anti-hacking safeguards" along with it "in an effort to curb online cheating," and naturally they've wound up blocking legit players from the game. The Injustice Facebook page did address this issue, though merely stated that it's being worked on, not that it's been resolved.
I fortunately didn't suffer either issue, though now I'm wary about launching the game again until there's at the very least an official statement, if not a resolution. If there are any further developments, I'll let you know.