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.
This is 100% it.
It’s the buildup to smiths moment of unleashed rage when he starts unloading the desert eagle at Morpheus as he runs to the helicopter and escapes.
Before this he was calm because he was in control.
Afterwards he loses that control along with his composure.