It's because, at that point in time, the precogs are offline.
Remember that, after finding out that Agatha was the precog who yielded minority reports, Anderton kidnapped her. Agatha is the strongest, and the other two precogs aren't able to function without her, bringing the system offline. Burgess took the opportunity while the precogs were offline to kill Witwer. His dialogue in the scene, just before he fires, calls attention to this:
Shh. Do you know what I hear? Nothing. No footsteps up the stairs, no hovercraft out the window, no clickety-click of little spiders. Do you know why I can't hear any of those things, Danny? Because right now, the precogs can't see a thing.