Just to clarify, the odd "ships show up on other planets on death" class of bugs are quite rare. Like they happened once, maybe twice in my last game which was about 60 hours (that I could tell, obviously it would be harder to track with AI ships, though I did have neinzul nests on in that game, but I think I only had one, maybe two "spontaneous" triggers).
Sadly, maddening level of rarity just makes it that much harder to debug.
I haven't tested the scouting thing with home planet exclusive stuff. Last time I checked, most of the "enemy ships on my/adjacent planet" effects don't trigger with scouts alone (I think there is only one spawning thing that wakes up when enemy ships are around is specifically designed around also waking up for scouts. No other build up and spawn when triggered thing is supposed to), so I would be somewhat surprised if core cockroach post (or whatever it is called) did it.
Maybe a minor faction that is enemy to the AI? That sort of thing has been an issue with several minor factions in the past.
