I always thought it was because the people who made the probe were probably aquatic dwelling, I.E. space whales, therefore they sent the probe out to explore aquatic environments, being nearsighted to the possibility of intelligent life developing on land. Similar to humans looking for air breathing land intelligence because that's the most familiar thing to them.
The harm it caused to Starfleet was just because it was looking in the oceans for life that communicated like whales, and not land based primates. I think it probably would have left once it determined there was nothing there, but it was probably programed to be thorough, and in the meantime it was throwing Starfleet into chaos.