The Amityville Horror was "based on a true story" too. People using the Amanda Knox story "based on a true story" are telling it as if she was guilty, when she wasn't. Just saying.
But if you think the show was 100% factual, did you miss the part about ART+COM losing in court? You choose not to believe that part, or think the filmmakers knew what "Brian" was thinking without ever asking them.
They admitted in a vanity fair article that they didn't think it was worth checking the other side of the story for factual accuracy.