Until they have granted you Friendly or Allied status, military class ships on their sensors in systems they consider theirs will lower their diplomatic rating for you. There is a bug where commercial classes sometimes also do this, even if they have granted you trade access, though that has been fixed in 5.50 I think.
For identifying Precursors there are several ways. The most straight forward and least likely way is to achieve communications in which case they will tell you that that is their name. The most likely is to pierce the armor of one of their ships at which point no atmosphere will escape. They've been removed in 5.50 but if you see one of the 25 megaton ships that is them. If their ships are in orbit of a planet without a population that is a good indication, especially if the ships run out of missiles and they come back to the planet to rearm.
