My theory based on some but limited knowledge of the case:

Amanda and Rafael were in the house, stoned out of their minds, at the time of the murder. They had nothing to do with it. When they discovered what happened, they took off in a panic for fear they'd be killed too.

Hence, no alibi.

After forty hours of nonstop police interrogation, people confess to anything. It's happened before, and not just in Italy.

Furthermore, the convicted murderer, whose DNA was found everywhere, including on the corpse, incriminated Amanda and Rafael in exchange for a fifty percent reduction in his sentence. He wound up with sixteen years for a heinous murder while A & R, with no substantive evidence against them, got a quarter century each.

It's worth remembering that as part of the Italian appeals process, actual judges were part of the appeals jury.

With no physical evidence, no reliable eyewitness, no motive, no prior record of violence or any wrongdoing, the original convictions were unquestionably miscarriages of justice. Regardless of what may or may not have happened, earthly standards were clearly served by the acquittals.