Sounds like it is in the finish layer or even between coats of finish.

What is the finish?

Some respond better to spot repairs than others (though almost all leave 'witness lines' at the edge of a spot repair since the repair sits on top of the old finish).

They may be showing up as the finish wears.

Another possibility is that workmen did track across partially cured finish or sealer and left a thin layer of dust. That dust might have blocked some of the UV rays which darken the photosensitive Brazilian Cherry...hence the footprints have become visible now that the floor has been exposed to light for five years. The dust blocked some of the UV rays...and now it appears as footprints in your floor.

That is my best guess...and I'm stickin' to it!

Glennsfc - interesting idea about the footprints masking the natural photodarkening. We have some areas (under rugs, for instance) that have never seen sunlight, and these are not as light as the footprints. So I don't think that is the answer.
I guess the next question is how to fix this? There are multiple such areas, each 2-5 sq ft. Anybody know if this can be spot-refinished, or will it require re-doing the whole floor?

Oh, man, that would ruin my day! What brand of BC flooring is it?

I don't think it is any special retail brand of Brazillian Cherry. It was custom flooring from a flooring company. I remember that the whole construction schedule was delayed becuase of a problem with shipping logs or boards or whatever from Brazil. We got tired of waiting and ended up using a different dimension of wood (shorter boards) as these were available. So that tells me that this was not a commercial retail "branded" flooring.

U definitely have a Ghost. Call ghost busters immediately

You may try the following on small area first:

Wet clean the floor with mineral spirits / paint thinner. Make sure to
ventilate and extinguish any pilot lights. Charcoal filtered face masks
for workers are recommended. Dry white cotton rags work well, and you
should see a visible yellow residue on the rags (oil residue). Wipe from
the clean area into the contaminated area, refolding the rags to wipe
with a clean face, and changing rags frequently.
Let dry, and clean a second time with a good water based surfactant
cleaner (like Bona / Basic cleaners). Repeat water cleaning until no
color transfers to the white cotton rags.
If the floor is tight with no open cracks filled with reservoirs of oil,
you may have restored the original appearance and gloss.
If this procedure doesn't remove all dulling film, you have greatly
increased the likelihood of a recoat succeeding by removing most of the
contaminant. If the floor is "open" with lots of cracks filled with
contaminant, it may require a resand and refinish.

@Shane Sexton is there a question?