The DNA could have come from earlier contact or even another article of clothing JonBenet Ramsey had been wearing prior to her death.
The first FBI agent to arrive at the scene of JonBenet Ramsey's brutal murder has revealed the catastrophic mistake made by police in Boulder, Colorado.
Ron Walker said early errors in the case of the six-year-old beauty queen found dead in the basement of her family home destroyed the case before it even got off the ground.
"Everybody makes mistakes at crime scenes, and I don't want to lay the blame on any particular person, but it was the philosophy in the police department at that time on the command staff that inhibited the officers and the detectives from doing the job that they knew they needed to do," Mr Walker says in Overkill: The Unsolved Murder of JonBenet.
His damning comments came in the latest TV special on the case, created by respected author Lawrence Schiller, which aired on Saturday on US channel Reelz.
Mr Walker said the biggest fault with the Boulder Police Department's investigation was the failure to interview JonBenet's parents Patsy and John Ramsey separately straight after her body was discovered 20 years ago, on Boxing Day, 1996.
"[People have] criticised the Boulder police for not doing what the police should have done on the 26th of December, and that was separate John and Patsy into two different interview locations, and get them interviewed, and get a full signed statement from them," he said.
'HER BODY'S LYING UNDER THE CHRISTMAS TREE' Police visited the home after a hysterical 911 call from Mrs Ramsey on Boxing Day morning reporting her daughter missing.
She showed officers a bizarre, three-page ransom note from a "small foreign faction", which handwriting experts say she wrote herself - although this has never been conclusively proven. The fact the sum demanded was similar to Mr Ramsey's annual bonus, the flowery language and apparently deliberate spelling mistakes also made investigators suspect the note was bogus.
Police later found the child dead in the basement, with a homemade garotte around her neck, a blow to her head and unidentified DNA in her underwear and leggings.
But it was weeks after the murder before police managed to conduct interviews with the Ramseys, who had by then hired a PR agent, flown to Atlanta and appeared on CNN.
Colorado reporter Carol McKinley told 20/20 in a television special that aired on Friday: "John Ramsey got on the phone right after his daughter's body was found, to his pilot to get him out of town. I mean, JonBenet's body is lying under the Christmas tree."
When Mrs Ramsey finally agreed to a formal interview, her manner was unusual, with the bereaved mother going on the attack instead of being defensive.
In police interview footage, an officer is seen telling her: "I'm talking about scientific evidence." She replies: "I don't give a flying flip how scientific it is, I didn't do it!"
Forensic psychologist and Boulder police consultant Steven Pitt told 20/20: "Patsy Ramsey's leaning in, she's right in his face. You seldom, if ever, see that.
"She was a formidable interview subject.
"Anyone who watches any beauty pageants knows we're watching people schooled in performing."
JUROR: 'I KNOW WHO KILLED JONBENET' Mr Walker's claim the crime scene was "mismanaged" comes after a bombshell interview with one of the nine grand jurors who voted to indict Mr and Mrs Ramsey on charges of child abuse resulting in death and accessory to a crime in 1999.
The juror, whose identity was concealed because his knowledge is not supposed to be shared with the public, said he "highly suspected" he knew who killed JonBenet.
But he said that while there was enough evidence to indict the Ramseys, he did not believe there was enough to convict them.
"There is no way that I would have been able to say, 'Beyond a reasonable doubt, this is the person'," he told the program. "If you are the district attorney, if you know that going in, it's a waste of taxpayer dollars to do it."
His comments explain why then-District Attorney Alex Hunter overruled the grand jury and chose not to indict the couple.
Mrs Ramsey died in 2006, but in July 2008, Mr Hunter's successor, Mary Lacy, went even further by clearing JonBenet's parents and brother Burke of the murder.
Ms Lacy said DNA on the girl's underwear didn't match anyone in the family. The DA apologised to the family for their ordeal, saying the tests pointed to an "unexplained third party".
NEW ROUND OF DNA TESTING In a dramatic development that could offer a glimmer of hope the case may yet be solved, current Boulder DA Stan Garnett revealed on Wednesday that his office was going to retest DNA found at the scene.
"You can find things out with certain analysis now that a year ago, two years ago, you couldn't have done," he said. "We have an obligation on every case to make sure we're doing up-to-date analysis."
An investigation by the Boulder Daily Camera and local news station 9NEWS uncovered "serious flaws" in Ms Lacy's interpretation of previous DNA testing.
Experts disputed the former prosecutor's conclusion that the minuscule amounts of genetic material found on JonBenet's the leggings "matched" the DNA in her underwear and that it must come from her killer. They said the "touch" DNA came from at least two people in addition to the six-year-old, but could have been transferred to her clothing in a number of ways, including on the production line.
In another highly publicised television special from September, CBS's The Case of JonBenet Ramsey, a team of forensic experts agreed there were problems with the analysis of evidence gathered from the crime scene.
One member of the team, pathologist Werner Spitz, said he believed Burke, then 9, bludgeoned his sister to death and Mr and Mrs Ramsey covered up the crime.
Burke, now a 29-year-old software engineer, strongly denies the claims and in October filed a defamation lawsuit against Dr Spitz, who he claimed was a publicity seeker "with a history of interjecting himself in high profile cases". He sought a jury trial and at least $US150 million in damages.
A hearing on Dr Spitz's motion for summary disposition is scheduled for February 24, 2017.
'BUTT-PRINT' OUTSIDE JONBENET'S ROOM The family has always blamed an intruder who came through the open basement window, a theory Ms Lacy said she was convinced of after a walk-through the Ramsey home in the days after the murder.
In her only interview on the case, in October, the former DA told journalist Ms McKinley, reporting for ABC News in the US, that the group saw a "butt-print" outside JonBenet's second-floor bedroom. "The entire area was undisturbed except for that place in the rug. Whoever did this sat outside of her room and waited until everyone was asleep, to kill her."
The grand juror who spoke to 20/20 also mentioned an unsettling "field trip" to the Ramsey home. "The basement in which she was found, it was a very eerie feeling," he said. "Like someone had been killed here."
Psychologist Steven Pitt told Overkill there was "friction" between the Boulder Police Department and DA's office because police did not believe there was an intruder while "some people" in the prosecutor's office did.
In a chilling 20/20 interview from three years after the murder, the first Boulder detective on the scene, Linda Arndt, said she had "a non-verbal exchange that I will never forget" with Mr Ramsey after he carried his daughter's body up from the basement - a crime scene contamination that should never have happened.
"He asked if she was dead and I said, 'yes, she's dead', and as we looked at each other I remember - and I wore a shoulder holster - tucking my gun right next to me and consciously counting, I've got 18 bullets," she said.
When asked why she did that, Ms Arndt replied: "Because I didn't know if we'd all be alive when people showed up."
Mr Walker still doesn't believe there will be a conclusion to the case: "The way the crime scene was mismanaged really dictates the case can't be and won't be solved," he said. Others still have hope, with pathologist Michael Barton telling 20/20 he had seen it happen.
"Things come up years later, decades later that sometimes help solve old cases," Dr Barton said.
Twenty years after this murder, the world is waiting for the new DNA results with bated breath.