Posting on the official Metal Gear Portal Site, Konami has explained that there is a situation where progress through the game can be halted due to the actions you choose to take. More specifically, game progress can stop if you choose to have Quiet as a buddy for Mission 29 and Mission 42. If you don’t use her as a buddy on those missions, the game breaking bug is avoided. No further detail as to what exactly happens in these missions (with Quiet) to break things has been forthcoming yet.
Konami will no doubt be working on a fix for this problem, which is confirmed as occurring on all versions of the game including PS4, PS3, Xbox One, Xbox 360, and PC. Chances are, the majority of players haven’t made it to Mission 29, let alone Mission 42 yet. So if you’re playing keep it in mind. If you have friends who are playing, let them know about this as it could be crushing to get that far into the game only to have to stop working.
If you’re playing The Phantom Pain, how far have you got and have you encountered this bug?