- In episode 4, when Mutio was "banished" by Verg, why is she still being held captive aboard the Phantom Ship during the battle? If she was banished, shouldn't that mean they'd make her leave the ship and not hold her there against her will?
- How was Katsuma able to stop the Chimerans from attacking Kino and Hayami's Grampus on the way to Zorndyke's village? Who was he to them? And why didn't he join them in stopping Zorndyke? Wasn't he the one that wanted to figure out what Zorndyke wanted in the first place?
Headscratchers / Blue Submarine No. 6