The game this happened in was a multiplayer game with a friend of mine.

There is an issue in the compound's coding somewhere which can cause them to spawn a massive amount of fleets. Fleet related mods that I use would be Gigastructures (Systemcraft and Planetcrafts) along with NSC2.

There rest of my collection, if you need it:
https://steamcommunity.com/sharedfiles/filedetails/?id=1382942350
The pictures depicting the end of the galaxy as we know it:
https://gyazo.com/10f454af2a98fd726877db88be69baed
https://gyazo.com/808fa96915c01251d607bed9a2ed6709

These fleets were able to wipe out the three planetcrafts that I had with my system craft in seconds. From what I could tell this put my game in an unwinnable state, the annihilator certainly wouldn't be able to wipe these out, the stream of fleets seemed constant at this point, like a fleet was spawning every day.

I couldn't begin the fathom a solution, just reporting on a game I did, I am not sure if the mod was ever put to this kind of test.

Edit: I should mention that this is on 1x endgame difficulty on a small galaxy.