Stacy kept on interrupting him and when he decided to confront her about it, she told everybody that he threatened her.
IIRC, she actually said he confronted her in a threatening manner, which isn't quite the same thing. A threatening manner could be just her perception. An actual threat is usually more clear. I agree with Bill that we'll never really know, as what we saw looked like a reshoot to me. I suspect the camera crew was covering the meeting, Stacy ducked out for a moment, and Brent took the opportunity for a quick off-camera confrontation. But, it turned out to be important, so we got what we got. There have probably been a lot of times over the seasons when something had to be redone for the camera, but probably not where it mattered so much exactly how things originally went.
I think it is incredibly lame to bring someone to the boardroom because he had an idea that everybody agreed to (including the PM) and which turned out to be a bad idea. Lame, lame, lame.
Yet, repeatedly, that's what Trump wants. Understandable if you presume that he really doesn't know what he's doing and doesn't want people who might bring him bad ideas, because he wouldn't know the difference.