A few times I've opened the app to see the ship in the dock, with the pirates-icon floating above it, when I knew I should have still been at sea on a voyage. When I went to the map, it displayed correctly. And then when I returned to the island, the "Gone Exploring/Back Soon" buoy had replaced the ship, as it should have been when I first booted. It's a fleeting problem even when it happens. If I reboot the app after the above process, the ship appears correctly "away" again when it loads back up. So it's not a game-ruining bug...but I also haven't been brave enough to try doing something I'm not supposed to be able to do when the game is in the bad state, like click to return the pirates to the tavern. Seems like that's asking for a crash at least.
Happened to me once, it's usually due to bad connection or connection interruption. Nothing to worry about.