The best type of paint to use over a rubber applique is chalk paint. If you are using a self styled or latex, even mineral paint, you will need to prime your applique first. In fact I recommend doing it anyway for the best result. Some spray paints don’t stick to rubber, and you can still use them, just prime it first.
Paint a thin layer of gesso or chalk paint and let it dry, to give it some stick. Once it dries you will find you get even coverage of paint of the item.