Reports indicate that government bureaucrats are using the security clearance process to block key members of the Trump administration from accessing sensitive national security information. The politicization of the security process is a signal that unelected government insiders, not the appointees chosen by the elected Trump government, are ultimately in charge of the nation’s military.
Earlier this year in The Washington Times, intelligence expert Angelo Codevilla wrote that the CIA was insulting the president by blocking security credentials for Trump appointees.
From his piece:

The CIA has denied a security clearance to Trump National Security Council (NSC) official Robin Townley without any allegation, much less evidence of disloyalty to the United States. Quite simply, it is because the CIA disapproves of Mr. Townley’s attitude toward the agency, and this is unprecedented. President Trump appointed Mr. Townley to coordinate Africa policy at the NSC. The CIA did not want to deal with him. Hence, it used the power to grant security clearances to tell the president to choose someone acceptable to the agency, though not so much to him. This opens a larger issue: Since no one can take part in the formulation or execution of foreign or defense policy without a high-level security clearance, vetoing the president’s people by denying them clearances trumps the president.
Hence, if Mr. Trump does not fire forthwith the persons who thus took for themselves the prerogative that the American people had entrusted to him at the ballot box, chances are 100 percent that they will use that prerogative ever more frequently with regard to anyone else whom they regard as standing in the way of their preferred policies, as a threat to their reputation, or simply as partisan opponents. If Mr. Trump lets this happen, he will have undermined nothing less than the self-evident heart of the Constitution’s Article II: The president is the executive branch. All of its employees draw their powers from him and answer to him, not the other way around.

Evidently, the president didn’t get rid of those responsible.
The Washington Free Beacon reported Thursday that officials within the intelligence machine have again made a decision about security clearance based not on the nation’s best interest but on bureaucrats’ desire to damage the president’s ability to lead effectively.
From the piece:

Adam S. Lovinger, a 12-year strategic affairs analyst with the Pentagon’s Office of Net Assessment (ONA), has been on loan to the NSC since January when he was picked for the position by then-National Security Adviser Michael T. Flynn.
Lovinger was notified in a letter from the Pentagon on Monday that his Top-Secret, Sensitive Compartmented Information (TS-SCI) clearance had been suspended and that he had to return to the Pentagon.
The letter cited unspecified outside activities by Lovinger. The notice said the suspension was approved by Kevin Sweeney, chief of staff for Defense Secretary James Mattis.
One official said Lovinger was targeted by Trump opponents because of his conservative views and ties to Flynn, specifically his past association with the Flynn Intel Group, Inc., a consulting business.

The report comes on the heels of a Monday revelation from the outlet that politics are increasingly playing a role in the intelligence community’s decision making process.
Free Beacon reported:

The blocking of security clearances under Trump contrasts with the handling of clearances during the Obama administration when a key liberal adviser with a questionable security background was given a high-level clearance.
Ben Rhodes, the White House deputy national security adviser for strategic communications under Obama, was denied an interim TS/SCI clearance by the FBI in October 2008, according to an email obtained from John Podesta last year.
The email stated that Rhodes was the only White House official out of 187 prospective White House aides to be denied the interim TS/SCI clearance.
Yet, despite the denial, Rhodes would later be granted access to some of the most secret U.S. intelligence information and emerge as one Obama’s closest aides who boasted of a “mind-meld” with the president on various issues.
Rhodes became one of the most active originators and shapers of key American foreign and national security policies under Obama.

The push-back Trump is openly getting from intelligence insiders helps to explain his total reversal on many foreign policy promises since the election.