Last week, Defense Secretary Jim Mattis was exploring whether the Navy could intercept and board an Iranian ship to look for contraband weapons possibly headed to Houthi fighters in Yemen. The potential interdiction seemed in keeping with recent instructions from Mr. Trump, reinforced in meetings with Mr. Mattis and Secretary of State Rex W. Tillerson, to crack down on Iran’s support of terrorism.

But the ship was in international waters in the Arabian Sea, according to two officials. Mr. Mattis ultimately decided to set the operation aside, at least for now. White House officials said that was because news of the impending operation leaked, a threat to security that has helped fuel the move for the insider threat program. But others doubt whether there was enough basis in international law, and wondered what would happen if, in the early days of an administration that has already seen one botched military action in Yemen, American forces were suddenly in a firefight with the Iranian Navy.

Ms. McFarland often draws on her television experience to make clear to officials that they need to make their points in council meetings quickly, and she signals when to wrap up, several participants said.

And while Mr. Obama liked policy option papers that were three to six single-spaced pages, council staff members are now being told to keep papers to a single page, with lots of graphics and maps.

“The president likes maps,” one official said.

Paper flow, the lifeblood of the bureaucracy, has been erratic. A senior Pentagon official saw a draft executive order on prisoner treatment only through unofficial rumors and news media leaks. He called the White House to find out if it was real and said he had concerns but was not sure if he was authorized to make suggestions.

Officials said that the absence of an orderly flow of council documents, ultimately the responsibility of Mr. Flynn, explained why Mr. Mattis and Mike Pompeo, the director of the C.I.A., never saw a number of Mr. Trump’s executive orders before they were issued. One order had to be amended after it was made public, to reassure Mr. Pompeo that he had a regular seat on the council.

White House officials say that was a blunder, and that the process of reviewing executive orders has been straightened out by Reince Priebus, the White House chief of staff.