This has always been a problem when Republican administrations have taken control. Over the years the bureaucracies have become saturated with left leaning career employees who form the guts of any federal organization. They are always there to work against the conservative appointees and to make them look bad. These career employees are a major part of the swamp. Recently, Obama made a big deal of filling every career opening with one of his socialist ideologues.
That goes to the Truman and Roosevelt administration “listening” to the senior-level (communist) State Dept officials who gave China to Mao’s dictatorship. Vietnam as well?
IIRC, there was a story out of the State Dept after the 2004 election. The person in control of a meeting said ‘President Bush has won a second term and we owe him our allegiance’. That person left the meeting and the second in charge said ‘And John Kerry came in second and WE owe HIM our allegiance’. The Leftists ALWAYS work to undermine Republicans in the highest levels of Government.