Why "What were you doing?"

Question

This is the clip blowing up the elevator from The Matrix (1999).

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.

Answer 1

The two in the room were doing something, but the two walking in were not aware what that was.

So when they walk in they ask what it was the people (or one of them) in the room were doing.

If they would ask What did you do? or What have you done?, this would imply that they did not walk in on an ongoing action (like talking, or interrogating), but that they notice that something has happened (which has now finished, but the evidence of which is present).

Both those options would apply is one of the people in the room would appear to be dead when the two men enter.

man enters room, sees other man and an unmoving body
What did you do! Why did you kill him!?
Don't worry, he's not dead. Just unconscious.

Since the assumption in the movie is that whatever the men were doing in the room was an ongoing activity, the question is not posed as if a completed action is assumed.

Answer 2

I think that in the context you mention what were you doing fits perfectly, I presume that these guys stop their activity when they see the police. So it refers to a continuos action in the past.