Discoloration on your towels may come from a few unsuspecting sources, such as the water in which you wash the towels. You may be able to avoid these occurrences in the future by adjusting the way you use some household items.
Makeup, Creams and Medicines
Makeup, creams or topical medicines could be the cause of those random marks on your towels. Makeup products or facial cleansers and creams that haven't been thoroughly washed off your hands before grabbing the towel sometimes leave pigment marks. Additionally, some acne medicines and similar prescription products can cause staining.
Watch Those Cleaning Supplies
A little bleach goes a long way, and it sometimes can affect things it isn't supposed to. If you have an automatic bleach dispenser in your washing machine, chances are there is residue in the dispenser. Every once in a while, this extra bleach may leak out in a load you were not intending to bleach, leaving discoloration. If you use spray bottles to dispense your cleaning supplies, the airborne droplets can affect the coloring on towels as they settle. Initial contact won't immediately change the color but as it settles, the particles can strip the color.
Your Water Supply
Look into the deposits that might be in your water supply. If the spots or stains are appearing after you wash the towels, there is a good chance you have mineral deposits that are affecting the towels. The deposits also might affect the walls of the washer and cause a rust build-up harmful to the color on your towels.