It appears your plants might be infected with Eriophyid mites, microscopic mites which live inside the flower buds and suck nutrients from the flowers.  This results in stunted and distorted flower parts, such as your "missing" petals.   Although normally the recommendation is to leave Echinacea seed heads intact through the winter to provide seeds for the birds, it is important in the case of infected plants that the plants be cut back to the ground in the fall and all plant parts (leaves, stems, seed heads) be removed from the area and destroyed to prevent re-infestation the following year. Do NOT compost these plant parts, but place them in a black plastic bag and dispose of in your garbage.

Here is an excellent article on Echinacea for more detailed information about growing healthy, vibrant plants: http://www.clemson.edu/extension/hgic/plants/landscape/flowers/hgic1182.html