Only ones that I've seen personally are the inconsistent changes in appearance of the Samurai characters. One scene, Orochi has an ornament, and then in the next scene, it's gone. (Samurai level 1, ending cutscene sequence), and Ayu's ornament also changes from the Descending Dragon into her own unique Gold Moths set. And in the same sequences, her Nodachi changes from Sasaki set to Tsubame, but in game it's still Sasaki.
Beyond that, the changes to each characters from the patches don't affect the story mode. Not that they need to.