Welcome blackbrc/Robert!
I would say these messages are related to threats of some kind, but I think I've seen them pre-Planet Buster. I get these at least twice every game (SP), usually several pop-ups in a row and then nothing, but occasionally the last one will pop up with the generic "This planet isn't big enough for the both of us" boast for that faction (the one you can't respond to anyway). If that's what it is everytime, I can't say.
It may or may not be a bug, but I definitely agree with Sevencubed that they can break your concentration, especially if you think you've just missed out on an unknown opportunity of some kind with the other faction, or made them mad(der).
When I first started playing the game several years ago, and before I realized there were more than a few bugs in the game, these pop-ups used to drive me nuts. I used to worry that I was missing some important communication, but they don't seem to change much in regards to the relationship between my faction and the other, so I just ignore them now.
If it's not a bug and this is the intent, it's pretty ingenius.
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"We are living in the future, I'll tell you how I know, I read it in the paper, Fifteen years ago" - John Prine
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