During the Deja Vu extra mission in the PlayStation 4 release, interacting with the prisoners in Chico and Paz's cells will cause both prisoners to die from Foxdie. After both prisoners are dead, the Fox Engine will appear to be under attack, and will then correct itself moments later.
In an early draft of the game's story, it was intended for Paz's dead body to be lying in the cage next to Chico, thus leaving him to watch her corpse gradually decompose over time.
In the side op Intel Operative Rescue, the player has to help an agent get into the helicopter. In the end cutscene, he is revealed as the creator of the Metal Gear series, Hideo Kojima. After the mission, he'll be in the helicopter in the main menu and waiting a while on the mission select screen will make him spin the list of missions.
It was originally intended for Ground Zeroes and Metal Gear Solid V: The Phantom Pain to be a single game, but the game's designer, Hideo Kojima, wanted people to experience the game near the launch of the recently announced next generation of consoles (PlayStation 4 and Xbox One). Ground Zeroes was also considered for the PlayStation Portable, but development proved to be much tougher than expected, and that version was cancelled.