I'm 100% certain there is either a rock beneath it or the water isn't deep enough.
The water is not flat nor the same height all the time like you're used to from other games... even at the coastline or at inland seas there a waves depending on the weather, which not only increases the waterlevel for a moment, but decreases it too before the next wave arrives (somewhat similar to reallife).
That's the moment where ships take damage.
Though, either dig deep enough, or build your harbor further into the sea or anker not directly at the coast and swim a bit.