If Bekka came down from space with nightblood and assuming she used it on some people when the radiation was critical then she made them nightblood and they could breathe the toxic air. Well if she's knew nightblood could do that why didn't she go back to her lab and use the people she injected to make more and more so everyone could have survived. She could of I guess just did it as a commander thing that's why she injected only a few..
Another thing I noticed was in season 2 when clark and Anya escape and they beat each other up Anya is bleeding on the arm and it's red, if she was the commander she should be a night blood... just a few things I noticed