I don't have SS08 yet, but in SS06 you see the same thing if you let the sim set up the static ships and AI ship routes. The static ships will sometimes be in the shallows or the edge of the shallows and you see them listing, etc. The AI ships will run into shallows, quays, etc. because of the route the ship takes.
If you don't tweak everything, you can expect such occurences.
WW