The prefix super- means “above” or “beyond”. A superscript is text that is higher on a line than normal text. A superset encompasses a set and items beyond the set.
The prefix hyper- means “too much” or “extreme”. Hypertension is too much blood pressure, hyperactive is an elevated amount of activity.
That said, there is overlap between the two meanings, and it often comes down to matching the Latin (super) or Greek (hyper) to its root.
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