It most likely are an NPR fighting the Precursor or Swarm, it should go away after a while...
One trick I have used is to start the game without any AI generated and with 0 chance to spawn any AI, only the Precursor or Swarm can appear. Then, after I have a decent sized empire I'm happy with I would use space master and generate a three to five good systems and then one powerful NPR in each of them. Still with 0 percent chance to spawn new NPRs. Once I have meet a few of them I could spawn a few more not so powerful NPRs in a few new systems to populate the galaxy some more.
That way you will not experience slowdowns until you have a lovely empire that is developed and you will have allot to do so waiting between turns will not feel like a waste of time since you are not waiting years between things you want to do.
Just a few tips...