Where there escape pods? If not you probably ran across one of the spoiler races Precursors, The Swarm, and Invaders all do not leave life pods, and Swarm doesn't even leave wrecks.
If there were escape pods, then you likely just had a fight with a normal NPR, they sometimes do leave fleets in place for years at a time, especially if skirmishing is happening regularly, and yes if you meet them outside their home system the game assigned name will not reflect their true home system even if you later discover it.
If I had to guess I would say you have a spoiler race though, especially if they significantly out-teched you.
To answer your other question there is nothing special you need to detect populations, they generate EM and Thermal signatures that are easy enough to pick up if you survey the system at all. Assuming you have EM and/or Thermal sensors.
It is possible to miss small bases though, a single DSTS and missile stockpile that is commonly left by one of the spoiler races only has a Thermal Signature of like 5, I often miss those until the geo survey ships come in.
