Piña coladas separate from the acidity in the pineapples and the fat in the cream of coconut. If you use all fresh real ingredients in your piña colada and it's allowed to stand, it will eventually separate.
An easy way to prevent piña coladas from separating is to add a dash of xantham gum or soy lecithin to the piña colada mix before blending. This will keep the mixture stabilized.