There's no need to start a new career - it ill work as long as you're not mid patrol.
I believe that the only ships that could cause the CTD are merchants as all scripted ships appear in game where they are meant to. I've been testing tonight and have found all of the merchants in career mode again except the Medium Old Oiler. If you're starting a new patrol then this ship shouldn't cause a CTD as, AFAIK, all harbour traffic is scripted rather than random.
What submarine are you using?
What base are you at?
What is the date of your patrol?
I'll try and replicate the CTD with the above info.
Also, try using the Harbour Traffic Lite mod and see if you still CTD. If so, I can rule out the scripted traffic in the harbour being a problem.
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