Nevermind, I got it fixed. You need to fill the ball with water all the way before putting the rest. It doesn't seem to recognize it if you work with it only half full and then top it off.
At the last level you only need to take the gate, then the ships and finally the other gate. Never let go of the gates! Then max your units and storm the center through the gates. That did it for me. You might need to take a few planets, as well.
A description for the upgrade items would be nice. Also, being able to pick up more than 1 thing at a time, less annoying music and a little more diversity. It's been only 3 levels and I am already bored.
Now it works =), thank you