Entering the gumball bonus stage makes you lose your shield. Not sure about the other ones.
The Knuckles MGZ2 boss still plays miniboss music (sounds a bit odd IMO, and I still wonder why they did that - accident or intentional?), and doesn't play the "break-wall" sound when the spikes penetrate the floor or ceiling.
Death Egg's bosses (Doomsday act 2 that is, I didn't bother looking at the ordinary boss yet) don't play boss music, they just play DEZ music. Also, when Robotnik flies away, everything is a lot slower than the final, and if you don't press anything you can get stuck in the bottom left until you go into debug mode.
Doomsday is really glitchy - I was in debug, so I don't know how many rings I had, but either I ran out of rings and died, or the zone just screws up when you beat the first stage of the boss. Either way, I died somehow, and when I used debug to revive Sonic again, the game acted like it was a normal level, and he just kept falling to the bottom of the screen. I re-entered the zone, created a load of S monitors and tried to break them (but couldn't, since you can't spin in that zone), and eventually it froze my emulator and X11 as well. o.O
When I play without debug mode on, it seems to work fine, although all the explosions are black...
If you kill Death Egg's 3rd boss while it's firing the laser, the laser stays on screen while he dies (not sure if this happens in the final, but I've never seen it happen).
In HPZ, even though your controls are locked during the cutscene, Tails' controls aren't locked, and he will continue to use his AI if you don't touch the second controller.
Pressing down in SSZ near to Knuckles doesn't make him wave at you yet.
This post has been edited by Hayate: 24 February 2008 - 06:51 AM