How exactly was Squeaky supposed to be killed, cooked, and served to Lord Skycrusher? She's a darkness creature, not a fire creature, wouldn't she just be teleported back to the Darkness Civilization when she was injured enough?
Why don't Raiden, Allison, and Gabriel wear the same clothing as the acolytes?
How come the Nature civilization refuses to acknowledge duelists? They call humans a myth (or rumor), but almost every other civilization is fully aware of them, if not knowing exactly what they are and what they do.
How were Ray's mom and grandfather frozen in place by the cyber-viruses? They'd never shown that power up until then, and didn't show it afterwards.
Hector makes a dark joke about exploding from mana overload and incinerating everything within a five-mile-radius. How exactly does he know this will happen?
How long had The Choten been working alongside the Council of Logos? Were they manipulated into helping him steal all Saguru's memories and make it impossible for him to retrieve them from the mother virus?
Alakshmi has a nightmare that her mother sold her to The Choten. Sure, she could have just meant "my mom paid some guy to take care of me because she didn't want me anymore" or "my mom turned me into a hired thug for some guy", but the usual meaning of that phrase (in the cultural context) is "my mom paid my dowry". Taking into account that in the dream, Alakshmi is clearly sitting in a young girls room and that she's currently sixteen/seventeen, holy shit. Doubles as Getting Crap Past the Radar.
It's heavily implied that "Piper" was never real. Either Megaria was just bluffing, or she really did shift into a human, marry Artie, and give birth to Allie.