You're talking about lawsuits, legal controversies and issues about how to apply the law. I don't see anywhere in said phrase you cite a mention the courts get to override Congress. In the Constitution, to the contrary, it is Congress alone that creates inferior courts, appropriates money to run them, and determines their jurisdiction and the sort of cases they hear.
(Denny Crane: "Sometimes you can only look for answers from God and failing that... and Fox News".)