Unfortunately this is an issue with Konami’s Metal Gear Solid V: The Phantom Pain right now. The publisher has recently warned that if you have the Quiet character as your buddy while playing Mission 29 or 42, it could potentially corrupt your save file. So much so that Konami has warned gamers that for those particular missions, you should not use Quiet as your buddy character.
This bug has affected all platforms that the game is playable on and according to Konami, they are looking into the issue to see if there is a potential fix that they can release. This is kind of a bummer as we’re sure that gamers would have loved to play the game the way they liked, without the fear of bugs and corrupt save files hindering them, right?
In any case since it only affects these two missions, we suppose it’s not that big of an inconvenience. Some of you might have already played through these missions just fine, but if you haven’t, this is something you’ll want to take note of.