I Keep Getting Super Deep Clogged Pores (closed Comedones) That

I keep getting super deep clogged pores (closed comedones) that turn into cysts deep inside my skin and they don't come to a head. Instead they stay sore and turn purple. I eat very healthy, exercise every day, wash my face with philosophy. I had perfect skin until about 2 years ago. I'm 21 now. I just have no idea what is going on!