How about the fact that the investigation almost immediately suspected Amanda based, according to Mignini, Giobbi and others, on her behavior, beginning with "the kiss". Because of this, virtually no one else was ever seriously considered. Mignini controlled how the investigation was run, and he almost from the beginning believed Amanda was involved, so why you think it not possible that Mignini couldn't "fix it so that two specific individuals get singled out" escapes me.
I'm curious, have you ever reviewed the fake wiki's "master list" of files? If you have - and I assume you have - then perhaps you could explain why there are dozens of taps, intercepts, etc., on Amanda and Raffaele's phones and conversations, as well as those of family and friends. It just doesn't make any sense to me why all those files exist for those two yet very few for anyone else if everyone was treated the same by the police. You'd think an open minded, honest person would review that list and conclude the police were almost exclusively focused on Amanda and Raffaele, but perhaps I'm looking at this all wrong.