The worst glitch i encountered in JenesisDS in the Sonic games was in Sonic and Knuckles in the Lava Reef zone last boss. The lava originally tilted diagonally in a mechanic to make the fight harder. In JenesisDS, the effect couldn't be properly emulated thanks to the DS hardware limits apparently. The lava just kind of obscured the screen when it tried to tilt, making the game harder. I wonder if this was fixed...
Original boss (tilt begins about a minute in)-
http://www.youtube.com/watch?v=H1SaAZfC6zY