Lloyd In future maybe post this in the iOS tips thread, as most of the guys in there seem to know what's going on with the console stuff as well now. Not me, as I don't have the game yet.
Anyways, I believe the "New Injustice App Unlocks" are telling you that things have been unlocked on your app version of the game from playing console. For instance by doing certain challenges or whatever on the console you unlock the character cards of Batman Beyond, Arkham Harley etc. on the app. It's not tell you you've unlocked stuff on the console.
Dunno bout The Godfall problem.