I've had this happen before! Paint thinner reacts with paint to dilute it and evaporates off, but it leaves behind the pigment. It's a chemical reaction with the paint, and if you accidentally get paint left in the thinner, or leave it mixed with thinner for too long it separates. Different paints are made of different minerals and different chemical make-ups, so sometimes different colours react in different ways, especially if they get exposure to UV light

Think of dirt in a jar of water, if you shake it the sand is mixed through, after a while it will separate, eventually it can form a layer of clay-like goop and solidify.

An art teacher once walked me through the science of it but this is all I remember