It's a bug that's been in the game since EA started but I've only ever seen it in multiplayer. A few friends and I have been playing again recently and you can literally sit there and watch the boat take dmg and clearly see that its not hitting bottom or rocks when the waves come in and no creatures are around. It just repeatedly takes dmg. 10 dmg, 10 dmg, 10 dmg.

It's not hard to spot because usually it sort of desyncs with the water and the boat doesn't change height with the waves. It used to happen while you were sailing but it seems like they fixed that part of it because from our recent playtime it's only ever happened while the boats were unmanned just sitting near the coast. Quitting out and reloading usually fixes it until it randomly happens again.


Side note: If you ever have to jump into deep water to get your floating boat materials back, MAKE SURE YOUR INVENTORY HAS ROOM. Anything you touch but don't pick up will sink. Learned that one the hard way.