When going to colonize a planet and your colony ship is in range, right clicking on the planet multiple times will result in two popups for colonization. Pressing "Yes" for both will leave you with a single colony that the game recognizes as two, leaving you unable to progress, as the game thinks one of the "two" colonies is always idle. This bug is easily reproducible on all races and galaxy sizes.

I suspect clicking multiple times for any action on the map may result in two or more instances of the event being spawned, so watch out for this nasty bug elsewhere!