Sunspots, vortices of gas associated with strong electromagnetic activity, are visible as dark spots on the surface of the Sun but have never been sighted on the Sun's poles or equator.
I agree with you that "which" does correctly modify "dark spots" because "on the Sun's surface" is a vital modifier here. However, "which" is incorrect due to meaning. We need a "but" because there's a contrast in meaning here: The sunspots are visible as dark spots, BUT they are not visible on the poles or equator.
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