The smoking gun was an error, but there were something like 9 Potti papers that ended up getting retracted. There's no way that someone could have accidentally made that many mistakes...
They were caught due to their bad behavior in the case you listed earlier. But Duke refused to do anything about it until Anil Potti's false claim of a Rhodes Scholarship came to light.
Fundamental methodological error -> "Come on, these are competent people, you have to trust that whatever error they made didn't effect the final result."
False claim of accolade -> "How dare you fucking try to pass off this garbage as legitimate science?!?!?"
It is intentional fraud, no doubt about it; they restarted halted clinical trials. I was just pointing out they did sloppy work too.