Not sure, maybe a little insect or disease issue. If you just can't prune it away, try some fungicide or insecticide.

What exactly is the problem? The foliage looks fine, and the stems don't appear to be having any problems keeping them that way. Blight can discolor stems, but usually blacken them.

Insects? Just look for them. If you don't see them, don't hose the plants down trying to kill insects that aren't there.

The closest thing that comes to mind is pythium (it can cause stems to look weird), but it's probably not that.

Were those stems ever rubbing against anything? Like rubbing against the supports until they grew above them? Looks like physical damage to me.