It's a quirk with the way the base game does empire names on the map I think, as I have seen similar occurances in vanilla games...

It seems to have something to do with empires that are spread out, whereby not all of their planets and outposts are directly connected, from experience...

I personally run a non-STNH mod that makes empire map names appear smaller, and addresses alot of this sort of weirdness... It's generally not recommended to run non-STNH mods with STN however, but I've never encountered any direct issues, personally...

This is a well-known glitch with the base game. If a system is annexed in such a way that it overlaps or is under some other part of the empire, the empire name effectively "wraps around" the entire map. It eventually goes away when other systema are annexed, but yeah, it's very annoying.