Without seeing a photo of the spotting it is difficult to give a good answer, but separation of the colorant or binder can occur when uncured paint gets wet. The effect can range from small dull spots all over a side to darker spots. Rain is a perfect example of this and I have had it happen to me.
One way to fix it, believe it or not, is to wet the entire surface with a garden hose then let it dry. If this doesn't work then another coat of paint is needed.