Hi - We had our plant pathologist and entomologist look at your photos. We are not sure what is producing this symptom. Aphids are a common problem on milkweeds but we do not see any in your photos. Asclepias can get fungal leaf spots, which would be more of a problem in wet, cool weather like we had this spring, but we cannot tell from your photo if that is the cause. Our recommendation is to prune out the symptomatic portion of the plant and discard it (in the trash, not compost). Asclepias tuberosa does push out side shoots and you can get another flush of flowers later in the season. Monitor new growth and send us photos again if you see new symptoms. 

Christa