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This may sound odd, but a certain glitch in Ed, Edd, 'n Eddy - The MisEdventures (SLUS_21260 U) cannot be replicated on PCSX2 1.2.1. The glitch involves firing a slingshot in First-Person mode at rats until the game freezes. Curiously, no such freezing occurs of the game in PCSX2.

I'm not sure if this should be a bug, so pardon me if this thread is perhaps in the wrong place, but I'd like to know why such a freezing of the game cannot occur on the emulator.
Perhaps PCSX2 has another advantage over the PS2?

could be broken disk. Are you sure that this bug is oficial and well-known and not only you are seeing this?
If yes it is still quite easily explainable with missing accuracy of pcsx2. Most of the time this missing accuracy will crash games... maybe once it avoids crashes.

My disc's scratch-free so I doubt that my copy is bad, but I also found a  YouTube video showing the glitch on the PS2 version of the game: https://youtu.be/4QOXHmdR4_Q?t=310.

The emulator has more "Freedom" to deal with unexpected things happening, since it's not directly limited by the constraints of PS2 hardware and the like. Couple that with some of the things PCSX2 does differently than the real console(for performance purpose or otherwise) and that's your likely answer.