As stated in the title: If you go to the Diplomacy screen and hover over the races planets you will get the wrong report tooltip and Faction coming up in the miniwindow (or conversely they are correct, but the wrong planet/logo is shown for them). For example in this screenshot: The Iconian planet is labelled as the Thalans and their faction leader is and details are shown. In this screenshot all the races are wrongly labelled except for the Minor races and the Yor. (there's a custom faction faction there as well).
If a save game is needed please let me know.