Continuity mistake: Superman punches Brainiac in the face hard just before taking Kandor from his ship. Just before this, Superman ripped the cords and pipes out of Brainac's head, and so his head is covered in a black goo liquid. When he is punched out cold, his head and face are still covered with it. A little bit later when Brainiac awakens, his face is suddenly clean.
Picture added by Quantom X