I've seen this problem. A pirate shipyard was leftover from a defeated AI player, and I could not direct fleets to attack it. However, one of the other AI players came by and attacked and destroyed it later on.
I can set rally points for shipyards to planets or to other starbases, but how do I set up a rally point in free-space somewhere?
[quote who="TurielD" reply="25" id="3558065"] Right now, while you can indeed place a bunch more ships on any one planet or base than a fleet can hold, it is far to easy to fly around defending vessels to get to the next planet in line. [/quote] That's the feeling I have so far. Parking ships in a starbase may defend the starbase, but that's not the point. The military starbase should exist to defend something else nearby, and at present, it basically can't.
It's controlled by your "logistics" capability -- this is a set total sum of ship logistic sizes that can be in one fleet. To put two fleets in one, drive them to the same square and then click on the "manage" button to the lower left. Then you can click, shift-click a,d etc., on ships to put in the same fleet.