Ships don't dock...

[Scarlet Hunter]

I haven't had that problem, ... perhaps you can allow yourself to be sunk if you can spare the repair bill.

I have noticed a similar glitch where my 'Drop Anchor' button sometimes stays active after I leave port, no matter how far I go out in the ocean. Then, when I get to my destination island and drop anchor, it takes me back to my departure port. I have found a workaround for this - if you get so close to your destination that you get the "Can't sail so close to land" message, then dropping anchor will put you at your destination.