Because Kryptonite is rock from Krypton.
I'm basing this on my vague memory of the movie but I think the logic is like this:
Superman grew up on Earth.
Not on Krypton.
Thus he would not be used to the Krypton environment.
Thus the radiation from Krypton rock would be harmful to Superman but not to humans (<- bit of a stretch there, I know).
Thus we need to find meteorites that crash-landed in the year that Superman arrived because they must (!) be from the explosion of planet Krypton.
A little bit of handwaving, bake for 30 minutes.
Voila!
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Spending as long as I do here, it's easy to forget that Oddworld has actual fans.
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