Why does "bloodfeast" work on Calca and Brina, who are essentially robots?
Edge keeps talking about how "history keeps repeating itself"; in fact, one of the major complaints about the game is that so many of its events were directly lifted from Final Fantasy IV. But then, you find out that the crystals were created to record the history of the world they were placed on. And if you talk to the crystals in the Lunarians' Tale, one of them even says, "Its history has been recorded. It must be revealed." So it actually kind of makes sense that everything is happening the way it did before.
Why is Rosa the only one to recognize the Hooded Man as Kain? The two of them knew each other as children, and grew up together. So she's seen his face before. But once he became a Dragoon he stuck to wearing his face covering armor almost all the time, so people that only met him once he started working the Red Wings or in the actual FF 4 story itself like Cid or Porom wouldn't recognize him without his armor on. Cecil would have likely recognized him too, but he's not in his right mind when the Hooded Man meets him (And he does realize who that was shortly afterwards, as Planet Eater shows).
How did Porom convince Kain to help her so easily? By accusing him of suppressing his loyalty to Baron. But she's actually talking to Dark Kain, his Shadow Archetype. That kind of argument hit him right where he lived.
Why does Edward have to travel between Kaipo and Damcyan by foot when in the original game he owned the Hovercraft that let the party ride across the shallows to get to Kaipo by sea. But then, what happened to the Hovercraft? Odds are you left it near Mythril last game, which has undergone a tidal shift with the Red Moon gone and the island is significantly larger. Edward doesn't use the Hovercraft because you left it out in the middle of nowhere and it probably got washed into the sea, You Bastard.
The CG opening both hides and spoils the identity of the Hooded Man. It doesn't openly reveal who he is, even when he's fighting Dark Kain, but if you recall the CG opening of the DS version of Final Fantasy IV, which this opening is pretty much calling back to, which character was shown after Yang and Edward, and before Palom and Porom? Kain
If The Creator has been creating and destroying worlds all this time, and the enemies fought near the finale are remnants of those destroyed worlds, and said enemies are from Final Fantasies I, II, III, V, and VI... then did The Creator destroy all those worlds?
In Edward's Challenge Dungeon, you find a NPC called the Adamantine Pig. Later on the dungeon, you are tasked to find it. When you find the Pig you take and give it to the NPC who tasked you with it. When the Pig is taken, another NPC opens the door behind the Quest maker, and prompty makes the Pig follow him. Talking to the other characters mentions that the room you are at is a restaurant. Now you must be thinking that the helpless pig you kidnapped is being turned into food. Too add more Horror, you are forbidden to enter the door where the NPC took the Pig.