Investigators focused on Riley's father, Kevin Fox, who was later cleared by DNA evidence. Kevin Fox served eight months in jail before the DNA test.
"I still had people coming up to me saying I was a child molester, a child killer," Fox recently told ABC's 20/20.
In Eby's case, investigators say DNA evidence, as well as the shoes, now connect him to Riley's murder. Eby is already serving time for another sexual assault.
"I think they deliberately did it because they didn't want anything to interfere with their theory that Kevin was guilty," said Kathleen Zellner, Kevin's Fox's attorney.
Zellner says she just became aware of the shoes within the last few weeks after authorities filed murder charges against Eby, the alleged owner of the shoes. She says the shoes were just one piece of possible evidence against Eby that investigators overlooked. The same DNA that excluded Kevin Fox now implicates Scott Eby.
"I think they should look into obstruction of justice charges because that's exactly what happened here," said Zellner. "They never even did a criminal background check. You would have seen that he had burglary convictions. You would have seen that he was on parole. You would have made a connection with the shoes at the scene."
Will County's sheriff apologized to the Fox family last month when Eby was charged. The current state's attorney has also apologized for his predecessor's handling of the case.
The little girl's body and the shoes were found in Wilmington Creek. Less than an hour after Riley was found in the water, a searcher discovered a pair of athletic shoes. The shoes had "Eby" written in the tongue. Experts say investigators could have easily traced the shoes to the Illinois Department of Corrections where Eby got them. He was on parole for burglary at the time.
Zellner says had the authorities looked at the shoes, the crime possibly could have been solved within days of the murder.
"When Will County looked at the shoes and looked at the tongue, they should have thought, 'boy, these are probably prison shoes. We need to find out who is on parole.' And the person on parole at the time was Eby," said Zellner.
It is alleged investigators also failed to fully investigate a nearby restroom where Eby has apparently told police he sexually assaulted the girl before throwing her into the water.
Eby has since confessed to the crime, saying he had intended to rob the Fox home just as he had apparently done at another house across the street, but he instead abducted Riley.
Kevin Fox and his ex-wife, Melissa, have been awarded an $8 million federal judgment in the case for wrongful prosecution. But the Foxes say they just wish investigators had pursued the evidence immediately so it wouldn't have taken six years to find the real alleged killer. They spoke to ABC's 20/20 last week.
"I'm still in shock. I have no words to even explain how I feel," Kevin told ABC News' David Muir.
"I needed to know what happened to her and what she went through," said Melissa. "He stole something very important from the world. She's gone. And there's not this amazing girl here anymore but there's disgusting people like him."
The FBI is now heavily involved in the case.
Eby has been charged with murder and criminal sexual assault. He is scheduled to be formally indicted for murder by the grand jury in court on Thursday morning.