Well this came out of nowhere. According to Konami Europe's official Twitter account, using Quiet as a companion during mission 29 or mission 42 can corrupt your save file. No further details have been given, but we thought that it was best to get the word out.
Quiet is one of the few buddies that you can take on missions with you in Metal Gear Solid V: The Phantom Pain. Her inclusion in these particular operations clearly screws something up rather badly, so we'd assume that this issue will be getting patched as soon as possible.