In this game, there were sprites that were unused that involved Sonic sneezing that are seen here:
http://info.sonicretro.org/images/4/4b/SCD_sneeze.pngThese sprites would have probably been used in the level Collision Chaos. There is a moth-like enemy (name was never given) that, when it flies, drops a trail of pollen, and Sonic would have sneezed when crossing it.
Also he sneezes in the opening animation of the game, but there is no sound. It is at 0:48 on this video:
https://www.youtube.com/watch?v=JCSL7naH-8A