Yeah, this is actually a feature. Any ships you have on autopilot will start moving when you click on the turn button, and if one of them reaches their destination with movement to spare, the game will pause so you can use that extra movement. Just click on "Find" to center on the ship in question and give it whatever orders you want. You can even go into your various management screens and do more adjustments, as your turn isn't over until all ships are done moving.
