I've encountered a problem where the cover won't spawn correctly in the room where you need to controll a worker droid to disable a laser barrier. The cover which is located on a wall above said laser doesn't actually emerge from the wall but instead remains the flashing indicator.
Whilst it does protect against the Boss neither it nor any other object in the room get vaporized however, even after reloading the checkpoint or reinstalling the game, making it impossible to progress as far as I can tell.