That's come up, too. The Copyright Office is a unit of the Library of Congress. Trump tried but failed to fire the head of the Copyright Office.[1]
U.S. Marshals used to belong to the judicial branch, and were hired by the district courts. In the 1960s, they were moved to the executive branch, under the Justice Department. This wasn't controversial at the time. The court system wasn't set up to train and manage the marshals. But the effect was that the courts lost their independent muscle.
[1] https://apnews.com/article/trump-supreme-court-copyright-off...
Related to this, there's a bill to move immigration judges from Homeland Security to the judicial branch, making them "Article 3 judges". That's currently considered unlikely to pass this session, but maybe next session.