Ok this is what happens:
This bug is very easy to duplicate. In normal conquest when an elite ground unit kills, it has a chance to produce a leader. I noticed the AI was using leaders to only rush buildings/projects, and I wanted it to build an army instead. I ended up replacing the combat produced unit to the regular army instead of the leader.
No problems yet, but the problem occurs when you add invisible ground units to the game. There is a chance that the human or AI player will be victorious in combat and create an army while there is an invisible unit on a nearby tile. Why a problem? Because normally if you move an army that's not been loaded yet in the direction of a unit the game will not let you attack because it has no offensive value. However with an invisible unit in the way when you try to step on that tile unknowingly, combat will be forced and the game is not coded to work that way.
An army can be attacked and it dies, but the game has a safe guard to keep you from attacking with an empty army. It just wont let you. The devs forgot to safeguard that unit the same way when accidentally stepping on invisible units, forcing a combat initiated by the army, making the game crash as it is impossible to happen.
I tried giving an empty army a combat value using Quintillus editor, and confirmed this even further. An empty army can't ever be the aggressor or it will crash the game. An army with an attack value of 1 and defense 1, cannot attempt to kill another unit, as the game is not coded to work that way. It creates a fatal error and it crashes. Even if the army has no combat value, stepping on an invis unit will force combat causing all kinds of errors.