Judges have pointed to the opinions of the civil service when striking down White House policies.

1. In halting the order (later reinstated by the Supreme Court), a federal judge declared that Trump’s justifications were “contradicted by the studies, conclusions and judgment of the military itself.” The judge inferred that Trump must therefore be motivated by illegal “animus” toward transgender people.
2. The person elected to head the executive branch was Donald Trump, not Sally Yates, and in a democracy all decisions must flow from leaders accountable to the people.
3. The Constitution vests the executive power exclusively in the president, but Trump probably felt that he was sharing power with a bureaucrat no one had elected.
4. President Trump attends a Department of Veterans Affairs event at the White House, August 3, 2017.
5. On January 30, 2017, Acting Attorney General Sally Yates announced that she would defy the White House and prohibit the Justice Department from defending the president’s “travel ban” in court.

https://www.nationalreview.com/2019/02/bureaucrats-civil-service-veto-presidential-policies/