Sounds like they are struggling with people that use different tactics to complete missions rather than the "right" way, or maybe people that do things out of order, killing an NPC that plays a part in a later bit of the mission, or completely bypassing parts of missions causing them to break.
The unpredictable nature of an open world, do anything game is causing them problems.
With the weather, the buddies, the wildlife, the tanks/choppers and all the different guards and bases it's probably a case of making them all work without impacting one another too drastically in a game breaking way.
Seeing how long it's taking to create Metal Gear Solid V The Phantom Pain, it was a wise move on Konami's behalf to release MGSV Ground Zeroes. The budget for this game has to be enormous. It's like Kojima is trying to create his own MGS version of Grand Theft Auto V (in terms of scale).