Idk if that's out of control or not anymore, what's a dollar worth? But I've avoided goodwill for Habitat for a while because there were various stories over the years about shady things. Now, they're big and basically all franchises so some of this was always gonna happen; lawsuits w/ racist/sexist/otherwise discriminatory managers will eventually happen once a company gets large enough, and franchises have a lot of independent control which leads to a lot of variance, good and bad, at different locations.
But they're also pretty shit at the corporate level: https://www.cracked.com/article_33357_15-impressively-evil-things-goodwill-has-done.html
So overall, on the astronomically low bar of regular evil corporate behavior, they're middling, but you should probably donate/shop elsewhere if you want to do the most good.
Now I know what my is gonna look like once fully grown!