A few days ago we learned that a certain glitch could corrupt your save file if you took Quiet with you as a buddy on specific missions. Fortunately, this has now been fixed, as reported by the official Metal Gear Twitter account:
Here is the full changelog for version 1.03 of the game on PlayStation 4:
At the moment of publishing this article the update is out for PS4 and PC, and is on its way for other platforms as well.
Source: Metal Gear Official Twitter, Wario64