When Dubaku redirects two airliners on a collision course, the pilots would have been warned by their onboard TCAS systems (Traffic alert & Collision Avoidance System). Onboard TCAS systems communicate directly with other planes in the area in the event that air traffic controllers accidentally (or in this case, deliberately) put two or more planes at the same altitude with intersecting headings. The system would warn both flight crews and give instructions on how to avoid an impact.
Nichols: Where's Emerson?
Tony: You're not going to be dealing with him today.
Nichols: What do you mean?
Tony: He's dead, So's Litvak and Bauer. I got them in the back room. You want to say hi?