The main explanation behind a lot of the reused enemies and bosses in the first episode is almost depressingly hilarious. Eggman is just on a really tight budget by this point.
At the end of the Sky Fortress Boss, Eggman and Metal Sonic escape the collapsing armada to return to the Death Egg. Sonic and Tails look around frantically and find a single pod, prompting them to squeeze into it. Not only that, but the craft itself flies into space in a shoddy manner and you can feel how uncomfortable the duo is inside. When they leave, they take the existing pod, as well as what is presumably Eggman's pod, and their return journey is a lot smoother as a result.
Eggman's display of trolling in Sylvania Castle's boss, where he reveals the twin arrow-shooting totems. However, instead of this being a boss fight rehash like in Episode I, he summons the TRUE boss, which promptly smashes the totems.
One the first stage of Episode 2, there is an item box a trollishly long way to the left.