What I noticed is, that it seems, that the ship is also placed deeper in the ocean when this happens. Also I had quite different anomalies with the sea. One time I had high spikes like towers, the other time big flat areas with stretched textures.
As they are flickering it is not easy to capture them on a screenshot. What always helped for me was to get back into port and restart game. So maybe it is something with saving & reloading the ships position?
Here 3 screens from one incident:
First I thought my Graphic card is dying, but its running ok all other things and looks good.
I know I have quite old PC, but its interesting, because most of the time everything is normal.
Win7 64bit
Intel Core2Duo E7200
4GB RAM
AMD HD6890