Sometimes rain can have different chemical compositions.
Sometimes it'll rain and if your car is slightly dirty and the rain is "clean" it'll actually wash your car, if your car is waxed/sealed.
Sometimes when it rains, the rain is "dirty" (by that I mean it has many sulphates and impurities which when left to dry naturally will leave watermarks). If you wash the car again or use a quick detail spray you should remove the watermarks with ease.