At the end, the baby's wings are missing when the old man holds her up.
Ulysses still had his space suit on after he and the children return to the bridge of the Odyssey at the end. But in the final shots he has his casual clothing on.
When Theseus picks up Ulysses's lightsaber, the hilt changes to a completely different design.
When on the bridge of the Odyssey with Telemachus, Ulysses is wearing his space suit in one shot even though he's wearing his casual clothing the whole time.
When Telemachus calls Ulysses, Ulysses says that "things are fine." But since he and Yumi are being attacked by an army of evil clones of themselves, and two more of the creatures are aboard the Odyssey, it's hard to see how things are fine!
Being in Cronus' palace seems to have aged Yumi; she's taller, has longer hair and shows, erm...development in some shots. Neither Ulysses nor Telemachus seem to be thus affected.