Haven't tried doing any of these things before the 1.1 Beta patch, so maybe not 1.1 issues:
1. When a ship is built at a planet with a pre-determined rally point, it is automatically launched upon being built, but it is not always displayed outside the planet. Clicking on the square where launched ships go reveals the ship.
2. Ships auto-piloting to a nav point which is set to Fleet which contains other ships causes the End Turn button to disappear (when they arrive at the nav and form a fleet) and the turn to break. Moving them there yourself doesn't cause this problem.
3. The colony nav point screen in the Civilisation manager doesn't seem quite right. Should I be able to select a colony in one column and a nav point in the other?