!!Dr. Robotonic is actually a separate character from Dr. Robotnik.

He was Robotnik's obscure cousin who tried to steal his thunder by building knockoffs of his machinery, including the Metal Sonics and the Death Egg II. This would also explain why he is [[YourSizeMayVary smaller than Sonic himself in this game.]]

!!The Sonic Clone is still alive.

It showed that it survived its encounter with Sonic, agitated, although the fate of it is not shown afterwards.

!!The eighth Chaos Emerald is actually a cloned Emerald.

After beating everyone else, Robotnik (or Robotonic) promptly clones your character, presumably Sonic, for a MirrorMatch. Upon defeating them, you then get the eighth Chaos Emerald. Considering everyone has Emeralds except you, as you don't start with one on your person, there's the chance that one of your Emeralds was cloned as well. Why the rocket needs eight Emeralds to begin with if there were only seven for real, however, is a different question entirely, unless your character was cloned in transit to reaching the rocket and thus conveniently got an extra emerald to help with the return trip as well.