They also quite clearly said Amanda Knox did it...
No, in a multi-layer judicial system they found her guilty in part and also later not guilty.
There is a difference between actions that can only be performed by 2 people and the probability that a specific person committed an act.
If one find someone guilty of shooting someone then that is based upon a presentation of evidence the fact a bullet went into someone's brain and killed them stone cold dead is not so disputable.