From what I know of the case, the two who were acquitted for self defense were not the men accused of standing over the injured and pleading lawmen and putting a bullet into each one's head at point blank range. Peltier was the one convicted of that.
It's kind of hard to argue self defense when your victim is helpless, bleeding and begging for his life.
From what I have heard, the prosecuter said no one knew just what role Peltier played in the shooting.