(CNN) Michael Flynn told Donald Trump's transition team that he was under federal investigation for secretly working for Turkey, according to a report Thursday in the New York Times . Trump went ahead and hired Flynn as his national security adviser anyway.

"Mr. Flynn's disclosure, on Jan. 4, was first made to the transition team's chief lawyer, Donald F. McGahn II, who is now the White House counsel. That conversation, and another one two days later between Mr. Flynn's lawyer and transition lawyers, shows that the Trump team knew about the investigation of Mr. Flynn far earlier than has been previously reported."

That wasn't the first time that Trump had been warned regarding Flynn. In fact, two days after his election, Trump traveled to Washington to meet with then-President Barack Obama -- a meeting in which Obama cautioned Trump away from naming Flynn as his national security adviser. "Given the importance of the job, the President thought there were better people for it, and that Flynn wasn't up for the job," a former senior Obama ad mi nistration official told CNN of Obama's decision to ward Trump off of Flynn

And, it wasn't the last time Trump was warned about Flynn either. On January 26, acting Attorney General Sally Yates met with McGahn, making clear that, based on what the Justice Department had seen, Flynn had been compromised by the Russians and was a potential blackmail target.

It took Trump 18 days after that Yates-McGahn meeting to fire Flynn. And when he did so, it was because Flynn had misled Vice President Mike Pence about the nature of his conversations with Russian ambassador Sergey Kislyak, not because of any of the warnings Trump had been given before and during his presidency.

Despite all of the trouble Flynn caused him, Trump continued to defend Flynn in public and private. In fact, Trump may have ensured the appointment of a special counsel to oversee the Russian investigation when he reportedly met with James Comey on Feb. 14 and urged the then-FBI Director to find a way to drop the probe into Flynn's ties to the Russians.

Why? Why would Trump name as his top national security adviser a man he knew was under federal investigation, a man he had been warned against by a sitting president of the United States? And then why would he keep Flynn in that job even after it was made clear to Trump that Flynn was lying about his contacts with the Russians and was vulnerable to being blackmailed by that country?

On its face, it makes zero sense. Trump hates when his subordinates make bad news for him. And he is quick to blame others for problems within his administration. So, what makes Flynn different?

Two things -- I think.

First, Flynn is a retired general. Trump loves to surround himself with military men and revels in his role as commander-in-chief. (It also probably didn't hurt that Flynn had been fired by Trump nemesis Obama.) If Trump defers to anyone, it's generals. That deference likely gave Flynn a far wider berth than the average staffer bringing bad news down on Trump.

Second, Flynn was one of the earliest and most outspoken supporters of Trump. Trump is someone who prizes loyalty above all else. And Flynn was there almost from the very beginning -- blasting the Republican establishment, leading the "lock her up" chants against Hillary Clinton and, generally speaking, doing whatever was asked of him by Trump. Trump liked that loyalty. And he wanted to reward Flynn for it. Everything else paled in comparison to that.

Prioritizing loyalty and military service is, of course, Trump's right. But for someone who premised a campaign -- and a presidency -- on his unblinking ability to not only pick the best and brightest but then to find ways to make them even more successful, Trump's misjudgment of Flynn seems like a major black mark.

His continued defense of Flynn -- well past the point of loyalty or even reason -- is even more baffling. Flynn is the origin -- or at least an origin -- of many of the major problems that threaten Trump's presidency. Everyone sees that. Everyone, it seems, except Trump.