This problem has been mentioned in other posts. It has been around for a while. I have seen it several times, but never reported it. I now have a save game one turn before it happens.
The problem is that when a race gives its assets to me, the colors of the assets are not all updated. Some that aren't updated do get updated later under certain conditions.
When the Yor surrendered to another race and gave me all their remaining assets, most of the assets still had the Yor color.

NOTE: Part of the problem can be solved quickly by saving the game and reloading the save. This causes many of the colors to be correct.
The long way to solve part of the problem is to do the following:
1. Move any ship into orbit around a planet, starbase or shipyard. This fixes the color of the ship, starbase or shipyard. It doesn't matter if the ship has the wrong color or the right color.
2. Start building something in a shipyard with the wrong color or shut it down. This fixes the color of the shipyard.
The picture of a ship at the lower-left of the galaxy screen and the small image of the ship at the bottom of the galaxy screen showing it at a planet, starbase or shipyard will still have the wrong color. The starbase management screen will also show the wrong color of any ship stationed at the starbase. The only way I have found to fix these problems is to upgrade the ship. Note that the upgrade screen will also show the wrong color when first upgrading the ship.
Since I do have a save game just before this happens, I have submitted it with more pictures and details on Ticket #KGE-572-36823.