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.