Firstly, I’m so sorry you encountered this strange game breaking bug! I’m not at home, but it sounds like the auto save combined with your prior movement in the previous level caused this. I think if you reload some later saves (ideally before you even started the mission) that should solve it. Apologies for the inconvenience caused.
Nope. Tried that. Didn't work. It's the third level of the hacking mission where you are in the facility with all of the artificials and she's going into the computer to release an EMP. It loads, she has a brief blurb about the security on this level, you are given a chance to save the game. Once you exit out of the save game menu, whether or not you save, she immediately has the same dialog bubble as if she ran out of time and the game over screen pops up.