It is my understanding that the game creates a 'tidal map' to match the outlines of islands and the way the ground is shaped on both sides of the shoreline, and that it's just not very good at doing so.
Probably best to wait for a storm on site to check if it is suitable for a harbor.

I have a small base on a tiny Peninsula where during a storm waves may come crashing through 10m above normal sea Level, it really is a mess at times