The time clock and sequence of events don't make a lot of sense. The plane goes down when the countdown clock was at 4:56, and Logan and Dariela start talking about sending a team 40 minutes later, which seems to be the same time the team comes up with a plan to look for a radio. However, it only takes them 15 minutes to find the radio, set it up, and reach the command center. Then when the IADG team gets in contact with the plane and decide to head out, the countdown clock is at 3:59. But then it shows them geared up and leaving, and then Logan talks to them as they are getting attacked, and the clock has run down to 2:35, suggesting it took them roughly 90 minutes to gear up and get there. When Dariela and Tessa get back in touch with Logan, the clock is at 1:50, and it's also still daylight. They leave to find another vehicle, get to the plane, the team creates the hormone diffuser, and Jackson and Sam head out, at which point the clock is now at 1:40 (and it's also nighttime), suggesting they were able to do all of that in ten minutes.
Jamie says the EMP took out anything electrical in and on the plane. If that were the case, they shouldn't have been able to open the cargo bay doors.