The color of your eLiquid can be affected by the nicotine content, 0mg may be clear in color while a 12mg of the same flavor may be dark brown. The color can also be affected by the oxidation process, which is a chemical reaction that occurs when the nicotine is exposed to oxygen. Exposure to light and heat can also affect the color of your eLiquid.
Steeping vape juice is a way of aging the eLiquid to remove any harsh bottled tastes and alcohol, which are volatile. Steeping mixes the VG/PG base, flavorings, and nicotine, and then oxidizes the liquid to remove the alcohol. The process of oxidation, while removing the alcohol, also darkens the color of the liquid.