[P.P.A.]

I was playing Sonic 3 & Knuckles as Knuckles. Died 2 times at the Mushroom Hill Zone boss (I just can't get used to how slow Knux is), but the third time Dr. Robotnik popped out of the ground instead of Eggrobo and it was him whom I fought. Wtf.

[Groudon]

In S3(&K) as Knuckles, you fight Eggrobo at the end of each act instead of Robotnik, so no glitch.

[CosmicFalcon]

Groudon, re-read PPA's post.

Also that is some mad hax. Perhaps Eggman was like "hey robo stop taking all my glory i want to kill him :("

[Crowbar]

Knuckles is slower?

[P.P.A.]

Knuckles is slower?

Well in that boss fight I had constantly trouble running or jumping back to the middle/right side of the screen (which I didn't have as Sonic or Tails).

[Combo]

I think something like this happened to me before in sky sanctuary.

[douglas]

Yeah, I've seen it a few times in various acts (not always concerned with dying, before anyone criticises my 1337 sk1llz0rz); strangely not so much on emulators as on console though.

[yse]

Knuckles is slower?

No, but EggRobo is faster.

[EngiNerd]

EggRobo is consistently faster/more difficult to beat.  I don't know about running speed, but Knuckles definitely can't jump as high as Sonic can, and that alone makes some bosses difficult.  However, Sonic Team deliberately designed Knuckles' playthrough of the game to be more difficult, and a large part of that was more difficult bosses.  It could be that the jump height, combined with the likelihood of accidentally gliding, makes that boss difficult enough.
Oh yeah, and one of the bosses ALWAYS shows Eggman, no matter who's playing.  IIRC it's Flying Battery.

[Crowbar]

Antiporcupine, you're correct on that last point. It's because it doesn't use the standard sprite (Eggman's facing towards the camera).

[CosmicFalcon]

Antiporcupine is also right about the general "Knux's game is harder", and I assume it's true to say that it's a combination of Knuckles' small jump and harder boss/level difficulty.

The idea I guess is to play through as Sonic then as Knuckles. So playing Mushroom Hill after you've beaten S&K, you'll want it to be that touch harder.