When I tried to survey certain anomalies which were defended by pirates, I was given the choice to engage or not.   So I choose not to with the survey ship as early in the game they cannot be replaced easily.

So I sent a fleet of ships to clear out the pirates by sending them to the anomaly.  I got the message that only a survey ship can survey the anomaly.  I think that the fleet should be able to clear out the pirates so that the survey ship can return and survey the anomaly.

I ended up having to put my survey ship in the fleet to both survey it and clean out the pirates.   It seems counter-intuitive to put an unarmed or weakly armed ship in a combat situation needlessly.