Those brown spots are normal in swamp milkweed, common milkweed, and butterfly weed - the pod may split open when it's still partly green or may turn brown entirely before opening. When I collect seeds, I wait till the pod opens and some of the "silk" is fluffing out, then cut off the pod (if you try to beak it off you might just lose all the seed), keep it in an open container in a dry spot (but not in a breeze or they'll all fly away) till well dried. To plant seed for next year, I just scatter it near existing plants as though it had fallen naturally. Here in Indiana the plants live over the winter and grow again for a few years, but I like to keep some young plants coming along. To put plants in a new spot, scatter seed in the fall in a dampish sunny spot and hope for the best. It doesn't matter whether the silk stays on the seeds or not. ....Sometimes I just keep an opened pod in a clear container like a Pyrex casserole w/ lid - turned upside down like a little exhibition case - in the house to admire the beauty of the silk, and the way the seeds lie in the pod.
