I ran into one of these as well. I had an NPR start in the system right next to my homeworld, who turned out to not be very friendly, as they blew away my contacting survey ship. They were in a binary system, the A component had a Precursor listening post in it, which I bypassed in the survey. The B component had the NPR, who was smaller population wise, and had a fairly small low tech fleet.
After the nasty NPR splashed my survey vessel, I wound up mining the warp point while my fleet trained up.
After several months, I moved back into the system and noticed the same thing. Nuke explosions going off. Apparently, the the NPR had moved into the A component and tripped across the Precursor warships that I missed. Precursors massacred the NPR and wound up nuking the NPR homeworld. I stepped in and splashed the Precursors, and wound up landing troops a couple of months later and seizing the NPR homeworld.