Intelligence in object avoidance is hard to find in SH3 ships. (unless it comes to torpedos
)So most likely it bumped into things during leaving the harbor, or maneuvering to the next waypoint. It might also just have been unlucky to negotiate right of way with a ignorant merchant that sailed on it's own.
Or it might have been the victim of an aerial attack by friendly planes that happend to be in the vicinity.
Sorry, no definite answer to this. Did they leave an autograph?