I mean the simplest and most likely explanation in my eyes:
Auba was late - frustrated Arteta disciplines him and strips him of the captaincy.
Auba takes this poorly and requests to be allowed to leave.
Arteta accepts this and subsequently isolates him.
There's plenty of circumstantial evidence to support this too. Understandable reactions from both sides imo if I am right.
Ultimately the main issue really is that Auba was captain, and you were never going to be able to strip him of that without blowing it up. It's pretty much identical to the Xhaka situation, except Arteta came in and changed his mind.