Make sure you did not actually delete the faces in 3ds Max. The script requires faces to be hidden (using the "Hide" function), not deleted. Also, ensure you are using the "MGSV Face Injector" script after hiding the faces, not before.
This is the more serious interpretation. A threat named "Hacktool.FaceInjector.A" has been identified and analyzed by security researchers at EnigmaSoft. face injector v3 work
If you are a gamer, you might be looking at a cheat injector tool that will likely get your gaming account banned. Make sure you did not actually delete the faces in 3ds Max