After fiddling with the faces of some NPCs in GECK, I got back into game and found that the tint of the face and their bodies do not match. In all the cases, the faces appeared brighter/lighter in colour in comparison to a darker body.

Does anyone know what is the cause of it and what ways are there to rectify it?

Not sure what causes this, but it happens randomly in the base game when you're not even messing with mods.. So I think it's a problem with the engine that would probably take a patch to fix.

Thanks for the information.