Konami released information on a big bug regarding the use of Quiet in Metal Gear Solid V: The Phantom Pain single player. This Non-Progression Bug described in detail here:
Until updated; please avoid playing missions 29 & 42 while using Quiet as your buddy, as this seems tied to the cause of the issue
— METAL GEAR OFFICIAL (@metalgear_en) September 8, 2015
If the steps mentioned above are not taken you could potentially ruin your save file. So take care everyone.
[ UPDATE ]
Looks like Konami has finally addressed this bug and a patch on all systems is now available for the fix.