Who stole my ship!

[Crimson Rose]

The past three times I've been on a materials run, someone has stolen my ship. How do I know? When I go to the shipwright to check for my upgrade, my previously-undamaged ship suddenly has damage. I try to get back on my ship via a dinghy, and my ship is now sunk!

I think I heard before from someone that you can stay on a ship and take it when it docks. How do you do this? And how can I avoid having someone do it to me?

Or is this just some kind of glitch? I note with interest that I can't board my war sloop when my war brig has been stolen.