Pilots
It seems there was very little research done on cockpit protocols and operation.
To see both pilots manually fly the plane, both with their hands on the wheel was laughable.
What were their feet doing? Fighting over the rudder?
Not to mention pilots don't manually fly a plane during the whole flight. Which they are doing BEFORE they travel through time. Obviously the auto flight systems won't work after, since it relies on GPS and becon information. Even before that, they are manually operating everything like they flying a WWII plane. Federal regulations actually require a majority of tasks to be done through the auto flight systems. Almost all take offs and landings are done manually, but after that most is turend over to the AFS..even though the pilots have to constantly monitor the system and adjust the controls to avoid things and make course changes.
Even without GPS and Radio Becons the autopilot would still work. Autopilot is just one part of the auto flight systems. It just locks the yoke on a set heading. The planes compass would still work. All they have to do is dial in a heading and engage the autopilot and their hands would be free. Manually flying the plane with all that was going on around them, would have been disastrous.