I had a similar incident. I died near my ship, I was investigating an island. But instead of respawning back in my bed on my ship, it got stuck and then it put me in a bed two grids away. I looked on the Company Messages and it said "ship removed" and "bed removed," as the last action.
i was angry to say the least as I had just dug up 2000 coins in treasure which was on a chest on that ship. I was at a Freeport so I quickly put a Sloop together and in an insane race against the clock made sail back to the island, hoping the chest was there.
The wind was with me and i sighed with relief when I saw the dead body marker. I also saw the ladder to my old ship standing up in the water with my crew bobbing in the water around it. The chest and coin were gone but I was able to recover my stuff from my corpse.
Lesson one, the ship bed is unreliable so any time I stop on an island I'm making a bed immediately (and naming it). Lesson two, make a chest on land and place your gold in it. Don't keep valuables on the ship if you can help it. Also, I am going to try naming the bed as the thought occurred that the system was confused as my ship bed just said "bed" and then it put me in another bed named "bed"
As for the ship, if its a bug and it seems so, I hope they fix it cause if I loose my new Schooner I will be real mad. I did wonder if the ship was destroyed by locals, but that seems unlikely since the messages suggest the game removed my ship. Atlas owes me 2000 coins.