This is a weird and obscure one, but - I started a game, played a few minutes, and realized I'd left the ship type setting on simple. I started a new game using the same seed and ended up with a different homeworld, and on the galaxy map the planets that had been adjacent to my previous homeworld were the yellow "I'm adjacent" color rather than white. I'm going to check to see if it survives saving and if so will post the save. It's not a particularly big deal, but does seem like a bug.
Edit - it looks like it's not just stuff adjacent to the starting world (although those have been scouted already by the time of this save - sorry!) Not sure what's going on.