Answer:
According to Webster, it is "minuscule", deriving from "minus"... So, "miniscule', while widely used, is considered to be errant.
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Minuscule is the traditional spelling; miniscule is considered nonstandard by most and outright wrong by many writers, dictionaries, and style guides. A minuscule was originally a letter form such as we now call "lowercase". "Capital" letters of that era were majuscules.
Why is it "correctly" spelled minuscule? Because it derives from the Latin minus, not the prefix mini~.
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