Hi, 

It may be the shady conditions as common milkweed prefers full sun. Swamp milkweed can handle a bit more shade and prefers wetter soil conditions. 

This could also be from milkweed beetles. The grubs can bore into the stems. A native pest for a native plant so there isn't an insecticide or chemical you should use to treat them. You can cut the stems open and see if you notice the grubs. Or look for the red beetles. There are also red milkweed bugs but they tend to congregate on the leaves and seedpods. University of Wisconsin has a Common Milkweed Insects information page that has some good photos you can compare and look for.  

They may not come back strong with the shade so if you have some healthy plants you can try to move them to a sunny location. Common milkweed spreads vigorously by rhizome so if you move one or 2 clumps it can quickly fill in an area. Just keep that in mind for where you plant it - if you don't want it running wild.

Emily