I have this bug as well, it happens in every single game I've played.
Also related to this bug could be another one, where AI civilization's traderoute freighters are in the wrong position. For example, you see them two sqaures away from the home planet, you try attack the square they are on, but your ship instead moves onto the square and shares it, instead of combat taking place, but then if you order your ship to attack the adjacent squared next to the planet, that the trade route is going through, the ship re-appears in that square, next to the planet, and combat takes place. The freighter is being displayed in the wrong square.
