While Jo and Zoe are driving to town from the airport, the car windows repeatedly change from dry to wet with rain.
Despite the transfer of power from Fargo to Allison taking place, the eight-hour computer reboot that accompanied the transfer from Stark to Allison in Season 2 does not occur.
The countdown clock for the Astraeus mission shows "Time to launch: 106 days, 38 hours, 02 minutes, 13 seconds". Since days are 24 hours long, this would more conventionally be 107 days, 14 hours.
When Jo and Zoe are arguing right before discovering the comatose town, in the background it can be seen they are driving in the woods outside town, but then are suddenly on the main drag.
The GD computer core is in Section 5, which has always been established as military experiments and was previously shutdown prior to Tess's arrival.
Jo revealed earlier that she had been to Flight School. This would mean that she knows all about helicopters. She therefore would have known the best way to disable a helicopter is to shoot out the tail rotor. That would have stranded all three Consortium members and saved the GD data. Choosing to stun Allison/Beverly instead doesn't make any sense.
Also, with Jo being an ex Army Ranger, she may have stunned Allison/Beverly to keep her from taking the hard drive, but, being ex-military and the attack on GD a threat to national security, she should have shot down the helicopter after it took off, and been complete authorized because of the attack on a government facility, she probably would have been given a raise and a commendation.