There are too many to really list without possibly doing a second playthrough (which is not happening anytime soon, if ever) but if I had to do the big one, it would be this:

Quote Originally Posted by Elpizo View Post
Probably this:
Chapter 1 to 12: "We're not gonna do as you say Barthandelus!"
Chapter 13: "Well smurf that, let's kill Orphan."
I'm also going to add:
(SPOILER)The Ending, where everyone is saved by a last minute Deus Ex Machina (the power of Lesbian LOVE FTW!!!) and somehow everyone is cured of their l'Cie status despite the game saying that doesn't happen. Granted the sequel is going to address all this, but I feel having the end resolved by a Goddess figure (making this a literal Deus ex Machina) that is only mentioned ambiguously twice in an optional datalog that you can easily miss by not bothering with the Mark Hunts, is kind of a poor way to do this. Truly XIII is the height of writing in video games...