Can red onions be used in chicken-ginger soup?

I made chicken soup with ginger for about 25 minutes. The soup sat overnight and looked clear, great. Next day, I removed the ginger, then added chopped red onions, celery, and carrots and cooked the soup for another 45 minutes. The soup turned black - really! The red onions lost their color.

When I looked up "red onions" on the web, it said they lose their color in cooking, and if cooked (rather than used in salads), they should be grilled or cooked "lightly." I am wondering whether there is a health issue or problem when the soup turns black, as it did. I can tell you that it tasted delicious...and vavavum, I could feel the energy barreling through my body.