You don't have to assume; paying attention would suffice.
Racial disparities, emphasis on victimless crime, asset forfeiture, prison overcrowding, and oh, the fact that USA has a much higher incarceration rate than any comparable polity ever in the history of the human race.
A justice system is broken when people break the rules and subvert the intent of the system. But most of what you're pointing to is, instead, conscious policy choices.
E.g. a society is generally entitled to criminalize activities it does not want people to engage in. That some other people may perceive the crimes as "victimless" is neither here nor there. I'd imagine that very few people convicted of drug crimes are not in fact guilty of those crimes, because the evidence in those cases is usually overwhelming (e.g. caught with physical product in hand).
Similarly, the U.S. has had about 5-10x the murder rate of, say, the U.K., going back probably a century or more, long before the recent rise in incarceration rate. So the fact that the U.S. has a high incarceration rate does not by itself mean that innocent people are being put in prison.
Very little about American policy is "conscious" at the level of us simple citizens. Ignoring that, this is a neat morsel of sophistry! The hundreds of thousands of people who are imprisoned in USA, who would be free in any other nation anywhere ever, aren't "innocent". And why not? Because we define them to be guilty. Ingenious!
Except criminal justice policy is uniquely conscious at the level of citizens. Judges and prosecutors are elected local officials in most states. Three strikes laws were passed by public referendum in places like California. Polls show 80%+ support in favor of keeping hard drugs illegal.
And anyone is ever guilty only because we define it to be so. In the state of nature, robbing a store and killing the clerk is simply the stronger animal exercising its free will over the weaker. And if robbery is illegal because we say so, I fail to see how the robber is less guilty of the crime because one country punishes him with 3 years in prison while we punish him with 10.
It's not just us who consider robbery and murder to be crimes. Every criminal code in history has done the same (although there are often exceptions carved out, especially for murder in the service of the sovereign), and some have even instituted more severe penalties for these actual crimes than we have.
I don't see "don't smoke or sell pot" anywhere in the Ten Commandments.
Unless you want to assume that the court is so broken, it will willy-nilly convict innocents.
But then it doesn't matter much what the prosecutor does, then the justice system is utterly broken.