The infamous one: in its early days, the NSA was ordered to stop surveillance of US citizens. It went before the Church Committee and testified that the relevant sites had been closed for more than a year. This was a lie, bottom to top. The sites were actively operating as those words were spoken, and they weren't closed down until whistleblower James Bamford exposed the lie. https://theintercept.com/2014/10/02/the-nsa-and-me/
There's a list a mile long of similar stories. Court decisions, executive orders, and acts of Congress have bounced off these agencies without result.
I'd like to see examples, but I agree that you're not wrong in general. The agencies do respond to court decisions sometimes. My point is that when legal compliance is a coin flip and there's no way to check for results, you can't be sure that legal decision has changed anything at all.
There's still rule of law, and the executive mostly listens to what the judiciary tells it to do. For all its flaws, some of our institutions work pretty well compared to most places. I cannot think of another country where judges are able to overtake heads of states in substantial policy outcomes.