Wow, I've figured out the issue, in your last post you made me realize I am supposed to wait for the helicopter to actually move to the base in the overworld map, I had been clicking on the ATLAS base after the soldier equip screen and pressing launch combat team which causes the crash because we've already done that step?
I just waited for the chopper to get to the mission and the game is running fine, the crash just comes from the mission not being locked out while soldiers are moving to it.