According to the European Konami Twitter profile, bringing Quiet with you during mission 29 or 42 may possibly corrupt your save file. Konami is working on the situation at the moment and has said, that to avoid the game corrupting save, do not bring Quiet with you on those two missions.
Obviously this is not a permanent fix but I’m going to heed their warning. I’ve put four hours in and I’m about to start mission 7. I really do not want to lose those precious hours, as well as, that cute little puppy I tranquilized, and ballooned to Mother Base.