Water from spills, water from continual source leading to mildew (black) or decay (brown/white) or alkali (white) or bleeding up of adhesive. Urine (dark) from pets, wet diapers. Unprotected metal chair legs. Improper maintenance with water or harsh chemicals. Traffic pattern wear. Excessive harsh sunlight (wood looks starved near South or West facing windows). Light deprivation under area rugs, large low furniture. Be sure to observe if only one piece of flooring is affected, or does the stain continue across adjacent pieces. Oil soap residue.
Correct water source, let dry. Minimize sunlight. Relocate area rugs. Correct maintenance procedures and products. Dark stains, lightly abrade surface with fine sandpaper, feather out area, dampen cloth with 50/50 household bleach & water and lay on stain for 30 minutes, remove, let dry, re-color if necessary. Waxed floors, clean with renovator or paint thinner (combustible) and re-wax. Whiteness/cloudy surface finish, clean and buff. If all fails, screen and coat, sand and refinish, replace severe boards.