You can see Agent Jones placing an arm in front of Agent Brown in the background. How come? I never understood why. Is it because he "cares" about his colleague's safety?
The script direction is a little vague as to what's going on in the background, simply noting that
...Then with one quick strike to the chest he sends Agent Smith flying backwards.
For the first time since their inception, the Agents know fear
I'd assume the gesture was supposed to convey that fear in some fashion.