The chief executive of an organization of any size has two kinds of subordinates. In the military, the commanders of the component units are the "line," while the people in the chief commander's office are the "staff." Other organizations may use different terminology, but the distinction is always there in one form or another.
Relying too much on the staff and not keeping the line officers in the loop is a major error. In the very early days of the Trump Administration, some of the important line positions were vacant, and some still are, because of stalling in the Senate. The Acting Attorney General at the time of the travel restriction executive order was a dyed-in-the-wool leftist holdover from the Obama Administration. The extent to which the Secretary of Homeland Security was in the loop has been the subject of conflicting reports.
President Trump nominated some solid people to head the government departments, and the confirmations are coming in now, albeit delayed. He needs to use them and listen to them. That is not to say he shouldn't listen to his staff also, just not exclusively.
One senior Trump administration official said new controls have been put in place so that executive orders receive more vetting before they go out.
"There was this near-death experience," the official said. "People will think twice before they act on their own."