Hijacked?

[Red Nations]

I remember something similar that was happening a few months ago and supposedly this was fixed with one of the updates.

I and a friend had boarded a spanish ghostship from my war galleon. Something glitched while we were fighting the skellies and we both landed in jail on Port Royal I went to repair and launch the ship and was not able to launch, got the same screen you get if you teleport ashore while your ship is at sea with crew aboard and you open the shipwright screen. My friend and I were the only ones aboard the ship when this happened so my ship was still at sea with no one aboard. We actually launched one of my friends ships and sailed right up to my ship which was still at the location where we had fought the ghost flagship. I had to log out of the game and log back in to get control of my ship back.

From the sound of what you describe it seems more like your ship had gotten glitched than an issue with this crewman taking over your ship. Even with someone taking over the wheel the owner of the ship is still able to regain control simply by taking the wheel back. The only exception to this is during a boss battle. If the crewman was on a cannon rather than at the wheel then, he wasn't in control of the ship.

I never use the public boarding permissions feature as I don't care for having people who I didn't personally invite and don't know aboard my ships. I might reconsider this if they were to add a walk the plank feature to the ship controls, allowing us to get rid of problem crew members and stowaways.