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The layouts of Sonic 3's Special Stages remained untouched; all differences listed here are palette changes.
The Chaos Emerald obtained in the second Special Stage was recoloured to orange, likely due to its corresponding Super Emerald also being orange.
The sixth Special Stage's Emerald was changed to a slightly different shade of red. The difference is barely noticeable, but it's there.
And the seventh Special Stage's Emerald was changed from cyan to a light blue shade.
The palette for Sonic 3's hidden eighth Special Stage was changed.
Likewise, its Chaos Emerald was changed from another grey Emerald to the yellow Emerald originally featured in the second Special Stage.
The background colour for the Special Stage results screen was darkened.