Edit: Dam you @The_Gear, you hadn't replied when I started typing. Bet me to it 
!
Im just guessing, but with such a large map how many ships do you have or are across the game right now. im curious if there are so many ships there is a memory issue or something random like that when it tried to "spawn" a new ship onto the map.
My main reply however is I suggest going though the steps in the below link.
-General Galactic Civilizations III Troubleshooting
https://esupport.stardock.com/index.php?/default_import/Knowledgebase/Article/View/496/161/general-galactic-civilizations-iii-troubleshooting
If the main steps dont work follow the last two steps on 'Reporting an issue' and on how to use the Support tool to add important information such as the crash report to the ticket.
Although sending the crash report is probably going to be the most relevant thing to do, unless your system just isnt powerful enough to run a larger map.
