Yeah, I hold the ME responsible. Super Sonic's approach to Angel Island is the first time in 4,000 years that the Emeralds (or the Westside Emeralds, if you're a twosetsfag) have been brought within a thousand miles of the Master (and the Master's whole gimmik is to negate their powers), so the ME is particularly well-stocked with the ability to de-power the CEs.
Just approaching Angel Island leaves Super Sonic vulnerable as he flies through the ME's extended field of influence; so one punch from Knux is all it takes.
If it's the Master Emerald making Super Sonic vulnerable to Knuckles' punch, then wouldn't he have been vulnerable throughout the entirety of the game? I mean, outside of the last boss, I can't think of a single instance where Super Sonic was as vulnerable to damage as he was during the first cut scene...
Edit: Computer fail <_<