Several specific elements don't add up, mainly pertaining to the Wayne deaths:
1. Bruce Wayne was 8 in GK when his parents died instead of 12 (in Gotham they explicitly state this as his age.)
2. Joe Chill (who took the fall) was locked up a day after Bruce's parents were killed. In Gotham, Mario Pepper was the fall guy and got shot dead; but the real killer was Matches Malone who would later die two years after the event. (Ironically, Chill's unnamed cellmate mentioned in GK died after 2 years as well, also a pawn of the Court.)
3. Bruce never discovered the Court of Owls for himself until the time of his death.