In a playthrough several hours ago, this happened:
Overlapping points icons in the modal window AND I somehow have two capitols, here. :P
Huh. I'm guessing the planet selector didn't properly clear the capitol marker when updating the displayed planets. Could be something else though, hard to tell just yet. I'll add the issue to my list and take a look at it after I finish the panel queue.
Edit: Just realized what the other thing you were saying actually was. Looks like there are two sets of planets being displayed which is what is causing the points overlap. So issue isn't with the capitol marker at all, just that the last planets either didn't get cleared or somehow it added a second set of planets when it wasn't supposed to.