Agent Brown and Agent Jones walk back into the office where Agent Smith is 'questioning' Morpheus.
Agent Smith stands up hastily and looks shocked by their sudden entry.
Agent Jones : What were you doing?!
Agent Brown : He doesn't know (what's going on outside)...
Agent Smith : Know what?
Agent Smith plugs his earpiece back in, and looks at the other two agents.
I wonder whether he can say "What did you do?" or "What have you done?" instead in this particular situation?
"What were you doing?" implies it is a process in which something is clearly or implictly stated.(like, I was reading a book when it began to rain. I was reading it at six), but I cannot find an implicit signifying thing here.