I found something in the game, I don't know if its a glitch or if you did that specially, but look at this:
When you finish Green Hill act 1 with 50 rings in story mode, you can go in the 1st special stage and have a Chaos Emerald.
Then, you reset the game, play Green Hill act 1 in level select, finish with 50 rings or more, and go in the 2nd special stage.
Do that 6 times and you will have all the Chaos Emeralds in story mode in Gren Hill act 2.