- In "Gems of the Past", Nova Terron shows a clip of the stronghold, proving that he somehow can see inside it. Considering the fact that the Mysticons don't hide their identities, he should know who they are. But when Arkayna goes to talk to him later in the episode, he seems to know her only as the princess, not as Mysticon Dragon Mage.
- In "Mutiny Most Fowl", Emerald was worried about Zarya and rushed back to the stronghold before warning her about Captain Kaos. Wouldn't calling her be quicker?
- How does Piper's age work? We know she's an elf and probably has a much longer lifespan than the others and in one episode they celebrate her 110th birthday. However, in the flashbacks where she met Zarya, you can see they both were children and much smaller. Even if an elf ages 5 times as slow as a human, it wouldn't add up.
- Why did Zarya use her phone and Nova Terron's picture to unlock the door in the Astromancers tower, whilst Malvaron showed a few episodes earlier, whilst looking for Zarya, that he can morph his face into that of someone else.
Headscratchers / Mysticons