Since boats are very difficult to stop, players will be beaching them more often then mooring them properly. (Beaching the boats causes the boats to become disfunctional.)

Even coasting into the harbors, it's very difficult to prevent beaching the boats. I haven't tried it, but it might be best to try backing into the harbors in order to properly moor them.

Another option, if the boats just skims the bottom of the beach for a short distance while coasting, allow the boat to be able to be moved in reverse instead of permanently causing the boat to get stuck on the beach.

(Currently, it appears once the boat's bottom touches the bottom, the boat is stuck permanently.)