I couldn't really of given a rats piss about the plot so wasn't interested enough to spot any logic flaws concerning that. But a few other bits bothered me
The Adamantoises have chains around them... who put them there?
The archylte steppe is a dangerous place, but why would wolves be attacking behemoths? Wouldn't they prey on chocobos? And why are their teeny sheep... surely they're sitting ducks to just about every monster living there?
Has anyone else found any logic flaws?