There may be one thing worse than encountering an unregulated nanite swarm left behind by an alien civilization, and that's encountering the devices that are meant to regulate them, and that is programmed to attack and destroy all nanotech, that has gone awry or mutated and does not have the proper codes.
A well known historical instance of this was the Meerlinda nano-disaster
Meerlinda was colonised in 3189 by the Shiftwranger clade of tweaks, a minor clade mainly known for their sensory adaptability and fascination with fractals (due to their very altered perceptual system). They were on the lookout for a new world to settle, as they were under some political pressure back home in the Kess-Utumu habitats of Alexandria due to their presumed inefficiency.
The planet soon became an important trading colony with a high level of tech and close Negentropy Alliance affiliation.
In 3804 Meerlinda was attacked by "gremlins" which systematically eliminated all technology and killed the local ruling transapients... the effect was the exact opposite of the classic "Neutron bomb" in that bionts were left standing while all fell apart around them (of course this killed a lot of biologicals too, in ships and vehicles and hospitals). The planet plunged into the steam age for a while, until an ISO finally arrived from the Negentropy Alliance.
No refugee ships lasted long enough to reach other systems, one clue that the attack was not, as some had suspected, a well-designed virus or nanoswarm. The disaster was enough to frighten the transapients even more than the bionts, but eventually a combined effort by various concerned clades and AIs put forward a tentative hypothesis. This theory suggested that the "gremlins" were ancient, alien defence swarms left behind by the extinct unnamed species HIE072CZE, which seem to have followed a vec freighter to Darram's Star from a nearby largely unexplored system.
The HIE072CZE are known to have built autonomous weapons, some of which are still active, but no other viable examples of swarm technology from that source have been encountered, before or since.
The ramifications of the incident were felt in several ways. Beside added defensive and quarantine measures, there was also increased cooperation between the different levels of Terran life (some transapients now realized that keeping the other forms such as bioids around had a practical purpose when dealing with certain alien threats). There were related examples of AI support for Human-led Institutes, and it is now thought by some that the unnamed mid-level AI behind the scenes of the HIE is motivated by more than just curiosity about the past or philosophical questions about the lifespan of civilizations.