When the controller disconnects during the Customer Service training, player can't resume the game with the keyboard.

[Alien.]

I discovered this major bug accidentally when I unwittingly disconnected my controller during this training. After the controller is disconnected the game does not recognize the input from the keyboard and I'm forced to leave the game by either Alt+F4 or the Task Manager.

[Thirsty]

I'm having the same problem, but throughout the entire game. I'm using a PS4 controller connected through a cable, and apparently the micro-USB connection isn't sturdy enough, so even the slightest movement can make it disconnect for a second and cause the game to say "Controller disconnected." Now, this is a minor annoyance, but there's a chance for the game to just not even recognize any input after the controller is reconnected, not even input from the keyboard. Like you said, my only options are to Alt+F4 or the task manager.
It's really annoying, because it happens in the middle of cutscenes and I have to restart the whole sequence from my last save.