It's a bug, Wideasleep. Truth to tell, you really don't need the ship, as your characters can pretty much swim wherever they want to go. The ship prevents them from shark, barracuda, and crab attack (but you need those crab shells!)
To resolve the "stuck ship" syndrome, though: swim out into the ocean aways and cast "Create Portal." Now go back to the ship, click on the wheel to "engage" it, then cast "Teleport." Boom! Instant teleporting ship to the spot in the ocean...and now it's unstuck.
Cheers,
-Sazerac
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