Im willing to think that is black spot a disease that affects mainly roses

Could be cercospora, google cercospora on phlox for information.

Or insects. Phlox paniculata is a native plant, so sometimes insect damage shows up. Usually the insects move on and then you will see no new damage.

Phlox should be planted about 18" apart; they need really good air circulation. That helps prevent diseases. Some nurseries suggest you remove all but 4 to 6 stems per plant ( I have not done this, but my plants are only in their 2nd year).