Plot hole: When Tails is flying towards Prison Island for the first time, he spots Amy on the island surrounded by enemies after mistaking Shadow for Sonic. There is no explanation given for how Amy arrives on such a guarded and fortified island. When Sonic asks her later, she says that she hitched a ride with Tails in his plane, but she couldn't have, as Tails spotted her on the island as he was flying in.
Suggested correction: Amy was talking about how she made it inside the prison, not how she made it to the island. There being no explanation of how she made it to the island isn't really a plot hole either way. It's just something that is never explained.
Bug: In one or more of the water races for the Chao, there are some large red crabs moving back and forth on the side lines. When they move to the left or right, their claws raise up, and then they lower the claws. But as soon as the claws lower, they instantly vanish and reappear above them again and lowering once more.
Bug: In Chao Gardens, if 2 or more Chao lay down next to each other, their bodies pass right through each other.
Plot hole: On the first level when the giant truck comes out and tries to run Sonic down, if Sonic slows down, the truck slows down too, even to a crawl while still chasing Sonic. But its mission is to hit and flatten Sonic. No reason to have it slow down because the player does.
