I think it definitely has to do with the style of games--the size of the universe and the number of ships.
I don't see it at the beginning of the game. Only when the number of planets and the number of ships gets very large. Only on the two largest galaxies.
The problem once it starts doesn't go away by itself. I have to save and restart, look for my built ships, and then inevitably the next turn shows new ships--but only for that turn.
I sometimes will find 2, 3, 4 ships unlauched at a planet if I don't look for them earlier. This is on the biggest size galaxy where I have 200+ planets.