Factual error: The head scientist tells Tony that the pathogen can survive 2 hours and longer after to host's death. Assuming it is either virus or prion (a protein), it wouldn't be alive to begin with and could effectively remain in Jack's body indefinitely.
Factual error: Mid-air collisions are almost always prevented by Airborne Collision Avoidance Systems which have been incorporated in all commercial aircraft since at least 1973. These systems are independent of ground control. These planes would not have collided.