Al Capone was caught for tax evasion. A variation on this theme is to catch some minor cog in an organization and to accuse him of anything that you can think of. And then to offer him as way out if he provides evidence against his boss.
Such tactics have been used against the mafia and such fraudulent organizations as Enron. The big question of course is: what happens if the target really is innocent? In that case both the cogs and the prosecutor will be seduced to blow things out of proportion in order to achieve a guilty verdict. Monicagate was a good example of how - when there is no real accusation - the "suspect" can still be condemned.
And let's not forget the sorry state of American justice. In this "plea bargain" paradise the chances of being acquitted are comparable to those once in the Soviet Union.
We don't know what Mueller knows. But the facts that until now have come out about Trump and Russia do in my opinion not justify the means that Mueller is now using with the Manafort indictment.