None of this is new. There have been leaks about Trump not understanding issues from the beginning of his presidency, when Pence (possibly) had to tell Trump that Mike Flynn was compromised and had to be fired. Trump seemed to think he could shut down the investigation into his campaign's connections to Russia, but found out he doesn't have the power to stop investigations.
So, really, it's not news that Trump is frequently at odds with his advisers. We don't need a recitation of the scores of episodes. Vox has a fascinating discussion about who leaked to Bob Woodward, based on clues from the book itself. His main sources are all former advisers with the exception of Linsday Graham, the senator.
It seemed likely that Trump would blow a gasket over the twin strikes on his credibility. However, Trump actually handled it pretty well (except for his reaction in the first 24 hours). He took the stand that the NYT is steeped in fake news, and he's actually doing very well as president if you look at economics and policy initiatives like trade. He said that with seeming confidence, as though he was prepared with a strong defense that he found believable.
The motivation behind the anonymous NYT editorial is muddy. If you have to sneak around to stop Trump for doing stupid actions, why would you tell him and the entire country? Trump isn't strongly going after the leaker in his midst. No high profile lie detector tests. No one claiming to be the leaker, no one blowing the whistle on a fellow adviser. I think this leaker may not be identified. If so, he'll just be one of many leakers. Can't name them all, and definitely can't fire them all. Got to live with them.
Extras. Trump's advisers didn't know what White House counsel Don McGahn (a public employee, not a private lawyer) told Mueller in extensive interviews. Oh, more disarray. Surprised?