I saw this in all the 1.1 betas and in the final. Didn't realize the feature was there in 1.0 (if it was).
When you set a planet to launch all new ships at a rally point, every now and then they will launch the ship but not tell it where to go. Then the game focuses it and you have to give it orders. Seems to happen more often when a tech is finished and the research window pops up.