Edit2: probably solved. I didn’t understand that Brown is talking about Neo and Trinity’s attack.
Agent Smith is questioning Morpheus, trying to extract the codes to the Zion mainframe. Neo and Trinity have attacked the building in which Morpheus is being held, trying to save him.
(Office)
Agent Jones: What were you doing?
Agent Brown: He doesn’t know.
Agent Smith: Know what?
It feels too poignant to have a machine say this without there being something else to it.
Edit: what I mean is, a machine wouldn’t “retort” or be passive aggressive like this.
Smith take his earflap(not sure if it’s the good word)/ear communication device. It’s a « subtle » nod that Agent Smith is becoming more erratic and that he is becoming something else (the second film call him a virus), something not controlled by the Matrix. So when Brown say « he dosen’t know », he’s understanding that Smith was not inform that Neo and Trinity are attacking the building because he have disconnect himself
I like to think Agent Smith took out the ear piece because he was confessing he hates it inside the Matrix, ie he was becoming more human in his own little misanthropic way.
It will absolutely fitting with the wackovski’s vision and what they have said about the Matrix world