There has been a running battle between State Department and White House for at least 50 years. Secretary Pompeo is pretty much the head of State in name only. There is a huge bureaucracy of career individuals that are almost impossible to fire.
Henry Kissinger who served as SoS for Nixon wrote about the friction between the two. He said that State thought that they were in charge and pretty much ignored directives from the White House.
Some years ago, I lived in Manassas, VA. I had an acquaintance there who was a career Civil Service employee in Health and Human Services, and when “W” became President, she was a GS 15, but was not a Republican.
Her boss was, so she was removed FRom her position (shunted aside) and instructed to do nothing. She went to work every day, did nothing except manage her side E Bay business, and came home. Every day that W was President!
That, of course, is FRaud, but it is never prosecuted.
The Hell of it is, everybody in Washington DC knows that the out of office Party folks are there doing damage to the in office Party folks, (i.e., the winner), but nothing, under the rules, can be done about it.
I suspect that President Trump has a White House study committee working on the problem, and after he wins the 2020 election, a lotta heads are gonna roll!
I sure hope so!