After I got my first Chaos Emerald (orange) I went into Green Grove Zone act 2 and ran into Knuckles and thanks to muscle memory, I forgot that you can only get one emerald per zone. However, when the Special Stage begun, it used (I assume) SS 2's pallete and showed a Green Chaos Emerald at the end, but still stated I got an Extra Life. Now when I got the 2nd Emerald, the SS was using using SS 3's pallete and the Emerald was blue (but on the results screen, it was it's proper colour (green)
(I don't have any photos because I couldn't capture it in time, was using Gens GX on Wii)
EDIT: Welp, got to Volcano Valley and... well...
https://youtu.be/aJhKFY2mN2I