Rustykap

Not much you can do unless the owner of the building lets you inside to get to them, unless there is a way in from the top that is.

I have this problem too. I have someone's brig in my harbor. They pulled in and accidentally left their company so lost control of the ship. Unfortunately, they were the only member of their company. So now I have to wait for the ship to decay before I can put anything in that spot.