There was a paper on this subject by Kurt Nassau, of Bell Labs, in the 1970's. Versions of various technical depth appeared in at least 2 or 3 journals as I recall. The first one I saw was in Scientific American. As I remember there are basically 2 causes: (1) inclusions and (2) transition metal elements either as major or trace components. Without reviewing this, and perhaps other literature, I'd guess that prehnite color is due to minor amounts of things like iron or copper or vanadium, whatever was around in the depositional environment that could find a home in the prehnite structure.
There is a rare pure white Prehnite from the O&G Quarry in Connecticut, which would indicate that the green color exhibited in most prehnite is caused by impurities, and green isn't the inherent color. I have heard once that iron impurities are responsible for the green, but this is unverifiable as I don't recall the source.
Many years ago, veins of colorless prisms of prehnite were common at the Foote Mine near Kings Mountain, NC. Wish I had saved a few, but they were so common few people collected them. I've found a few stout, very pale green prisms in explosion breccias at the 3M Big Rock Quarry near Little Rock, Arkansas.