The olde "save game CTD" nightmare!
I personally don't think it has anything to do with proximity to ships or land. I frequently save close to port when heading out on patrol and those early patrol saves never give me trouble. However, once I sink a vessel for the first time on patrol or if I have been attacked, then any save I make after that point seems to ALWAYS CTD.
That's one of the reasons I play over the weekends now...start a mission on Friday night, leave it open all weekend, and end it in Port by Monday morning.