Hm, I have never seen flags added in the galactic map that I haven´t set myself (except for when I conquered an alien race or got system info by espionage). You sure you didn´t do it yourself by accident? There is a dropdown where you can select a "controlling empire" AFAIK, you have to mark system with aliens yourself.
If you did get the data from some aliens, I belive they mark any system where they have seen precursors/aliens with their respective empire, even if the precursors are long gone by the time you get to the system (the flags stay on until you remove them yourself)
