Based in the information you have shared, I am guessing that your Echinacea has one of two problems: mites or a disease commonly called aster yellows. It seems most likely that your Echinacea has eriophyd mites. Eriophyd mites attack the flower, while aster yellows impacts the entire plant. 

Here is a link from Ohio State University with a bunch of information and photographs. 

Right now, I would recommend removing all of the effected flower heads/buds and disposing of them in the city collected compost. Cut off the seed heads/flowers/buds and put them in a bag and keep them closed up until compost collection comes. Next year, monitor your plants closely and remove anything that is effected as soon as you notice the symptoms. 

Lindsey K. Kerr, MS, MHP (she, her, hers)
Consumer Horticulture Educator
Michigan State University Extension