The three biggest holes in The Case of JonBenet Ramsey documentary.

When the two-part documentary The Case of: JonBenet Ramsey aired earlier this week, a lot of people walked away certain – as the investigators were – that Burke Ramsey, JonBenet’s then nine-year-old brother, was guilty of her death.

But according to Rolling Stone, the documentary seriously misled viewers with arguments derived from an inherently flawed police investigation and biased statements about the Ramsey family. They even go as far as to describe the CBS series as a “witch hunt” intent on naming Burke as the killer.

Another criticism of the documentary and the conversations following its release is that, at times, we seem to forget that at the core of this case is a six-year-old girl whose life was tragically ended. In order to talk in great detail about the role of a torch and a piece of pineapple and a toy train track in the killing of a young girl, we’ve dehumanised her. And this adds another layer of tragedy.

But given the huge impact of the CBS documentary, it is necessary to consider whether the claims it made are fair. All over Reddit, Twitter and Facebook, people are vilifying Burke Ramsey, absolutely sure he is responsible for the death of his younger sister. Yet, according to Rolling Stone there are three main holes in the investigation seen in The Case of: JonBenet Ramsey that simply can’t be overlooked if we want to remain objective about bringing JonBenet’s true killer to justice.

The misleading analysis of Patsy Ramsey's 911 call.

The documentary opened with a review of the phone call Patsy Ramsey made to police in the early hours of December 26 1996. Criminal profiler Jim Clemente and behavioural analyst Laura Richards attempted to decipher an inaudible portion of the call, when Patsy thought she had hung up the phone but didn't disconnect.

They said they were using the latest audio technology to re-analyse the call, and were ostensibly shocked when they heard three voices (despite the Ramsey's having maintained Burke was asleep). They also claimed to hear a male voice say, "We are not talking to you," Patsy shout "Oh my Jesus, oh my Jesus," and a young voice ask, "What did you find?"

What they didn't disclose, however, was that none of this was new information. The same conclusions were drawn in 1997 by the Aerospace Corporation, and leaked in a number of publications. Clemente and Richards, therefore, were likely influenced by confirmation bias - the tendency to interpret evidence to confirm pre-existing beliefs.

The complete dismissal of DNA evidence.

A significant portion of the documentary was spent considering DNA evidence. Given that DNA, which is currently unmatched to any suspect in the case, was found on JonBenet's underwear, it was important to look at who this might belong to. For investigators in the past, the unsolved mystery of this DNA meant that the Ramsey family were innocent.

But Dr. Lee explained (and demonstrated) that touch DNA is easily transferred, such that DNA will show up on a brand new pair of underwear, simply from a factory worker.

While this is a possibility that should definitely be considered, it doesn't mean we should completely discount the DNA on JonBenet's underwear. Essentially, Dr. Lee's argument implies touch DNA evidence should be ignored in all criminal cases, because, really, it could've come from anywhere. But there are many instances where DNA has been a crucial part of solving a crime, and we shouldn't rule out this possibility when it comes to the death of JonBenet Ramsey.

Placing too much emphasis on behavioural and linguistic analysis.

The CBS documentary used a number of experts to comment on the behaviour of John, Patsy and Burke following JonBenet's death, as well as the language in the ransom note left in the house. Their analyses ranged from body language, to pronoun use, to vocal inflections and linguistic phrasing. But what wasn't acknowledged was how inherently subjective such interpretations are.

In prior criminal cases, we've seen just how wrong we can be when we judge individuals reactions to horrifying circumstances. Lindy Chamberlain was said by many to appear aloof and unemotional following the death of her baby daughter Azaria. But when she was exonerated years later, it became clear how incorrect our assumptions had been.

Categorising John, Patsy or Burke's behaviour as odd or abnormal is irresponsible, given we weren't given any indication of the validity of such interpretations, and whether they're taken seriously in a court of law.

In many instances, opinions were presented as facts, and one final theory (with no real physical evidence to support it) was ultimately agreed upon by the group of experts. Of course, JonBenet having undigested pineapple in her stomach is not enough to come to the conclusion that she took Burke's pineapple, and he got angry and killed her with a torch. But this is essentially what the documentary claims.

It was a fascinating series, with some valid arguments and compelling demonstrations. But it's important we keep the many shortcomings of CBS's documentary in mind before we start to vilify a potentially innocent man.

But ultimately, the most crucial thing to remember is that an innocent little girl lost her life. And that, undeniably, is the greatest tragedy.