Two from FFIV. I might stand corrected, but they seemed like plotholes to me.

Game: FFIV
Loophole/inconsistencies: Kain encourages you to press on in the Village of Mist because "we must rescue Rosa!," even though Rosa had not been kidnapped or otherwise threatened in any way at this point of the game.
Correct one: Um, changing Kain's dialog would fix that.

Game: FFIV
Loophole/inconsistencies: Supposedly, killing a summon will kill the summoner (hence Rydia's mother), but when you kill Golbez's Shadow Dragon (I'm under the impression it was a summon), he doesn't die.
Correct one: Maybe I'm wrong and it wasn't intended to be a summon after all. But that was the impression I always had. Maybe the dragon was just hanging out in the corner and Golbez was like "yo, c'mere and help me out now, minion."