First of all, I don't think Nicodemo was framed. He is a known gangster, he probably wouldn't be with the Philadelphia mob if he weren't "capable".

Yes, innocent until proven guilty still is the law, but judges tend to believe law enforcement over anyone else. I don't think they purposely frame people, but they are human and they occasionally make mistakes. I have never been accused of a crime, but have gone to court to fight traffic tickets, municipal court is like a kangaroo court, cops can testify to one thing, then contradict themselves two minutes later and the judge will say nothing about it.