Ferries don't seem to work properly in some places. I've noticed it most in the Iron Islands and trying to get to Braavos from the mainland. I have ships now so I don't encounter it, but I can do a little exploring if need be.
Are you sure you are using ferries and not harbours. Harbours are only for the AI and don't have a ferry system.
Yes, I'll get you some more specific info on it after I get a chance to play some more tomorrow.