We just released patch 1.2.1.14.
It fixed a bug where is certain situations would not allow players to attack the final enemies starbase even after defeating all the fleets in the star system.
For those who ran into this issue and your currently saved last game was when you first encountered this issue, it will now allow you to attack the starbase. When you mouse over it, it will still show you that you still have fleets left to defeat. But if you target it and move your ship there, it should update those fleets as being defeated, allowing you to attack the starbase.
However, if you left the star system and went into another one, and then viewed the star system view, when you go back into the original star system, you will have to defeat the enemy fleets again, as the info regarding the stat of the last galaxy you were in will have changed to the newer one.
Thank you for your patience.