Yes, happend to me too but not for a long time now. Regarding monster (spawn) you want to encircle your boat with fireplaces which surpress spawn within a 10 sqm range. I always place a fireplace left, right and in front of my boat. The more the better.

It can happen under sail with crew too, ships just love taking random 10hp knocks from what appears to be nothing. Definitely something to do with multiplayer lag.

Not sure is this is a help or what you mean, but I've noticed that boats can take small amounts of damage when moored by them crashing into the sea bed or shore if you're in shallow water when they move with the waves. A little bit over a time can destroy your boat if left there for a while. I've lost lots of boats this way. Also if you're close enough monsters will spawn and attack if if they can't get to your character.

It fixed itself, probably lag related bug. Thanks anyway.