[Mrs. Don-o]

That's not a problem, --- in those cases, because they are the result of the aging/oxidation and darkening of the lacquers and pigments used on the original art.

But 2 millennia of art show the irrepressible devotion of the artists in portraying Jesus and His Blessed Mother in the noblest and most beautiful ways they can conceive. This will vary by cultural epoch. There is nothing wrong with this. It is the homage of the artist's heart.

"...for Christ plays in ten thousand places,
Lovely in limbs, and lovely in eyes not his
To the Father through the features of men's faces.

--Gerard Manley Hopkins "The Kingfisher"

[Ruy Dias de Bivar]

I’ve read the darkening came from centuries of votive candles, much like the Sistine Chapel was darkened from years of candles, till restored.