Day 7: 1:00 PM - 2:00 PM - S7-E6
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.
Day 7: 6:00 AM - 7:00 AM - S7-E23
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.
Day 7: 9:00 AM - 10:00 AM - S7-E2
Factual error: Tony Almeida takes control of 2 planes to create a near miss. In reality all aircraft use a commonly available AM voice radio and pilots can hear each other's radio communications. It would be straightforward to contact the planes and warn them.
Chosen answer: Nobody knew, not even the writers, until at least halfway through the season when they were writing the end. They wanted to keep all options open.
Nick N.