This happened to me during a game using the production release 1.30

I had a stack of ships right next to the Drengin homeworld. Stack consisted of 2 fleets of combat ships, 2 fleets of transports, and one single transport. One combat fleet attacked the planet and destroyed one "orbital fleet" worth of ships. Second combat fleet attacked the planet and removed all remaining ships. 1 transport fleet attempts to capture planet and loses. Second transport fleet captures planet and still has unused transports left over.

BUG PART:
I now have a stack of ships sitting next to my newly acquired planet. I simply want to put all of these ships/fleets into orbit of the planet. Each time a ship/fleet becomes active, I right-click the planet to garrison it, however the thumbnails that show the ships/fleets in the stack never get updated. It still looks like I haven't moved anything.

This isn't a show stopper. If you click on the main map somewhere else and then click the stack again it will refresh properly.