I have the same problem on my dedicated server, and my galleon currently shows 3 different clusters of beds, 12 total, while only having 2 visible beds.
- They are all placed in the same room in the back, but if you zoom the map close enough, there are three distinct groups aka lists of beds to choose from. I have list of 3, a list of 4 and a list of 5. They are not always visible, sometimes at the respawn screen I only see the current beds.
- Choosing the bed to respawn at seems to be a game of chance, where if you choose incorrectly (I'm guessing if you choose a bed that has disappeared), the game sends you back to the home server and you must then spawn at a bed there, at which point you can fast travel back to the ship. I just remembered you can rename beds so I'll try naming the ones still present so I can differentiate and test better.
- I've only had 1 bed disappear on land, early on when I first started my server. It reappeared later and I haven't had any issues with land beds since.
- I've tried removing the "ghost beds" via cheat destroyall simplebed_c but only the visible beds get destroyed and the ghost beds continue to show up in the respawn lists.