1. You could give the ball an active boolean and set it true when the mouse changes from (0,0). Like this:
<img src="https://dl.dropboxusercontent.com/u/8367729/construct/pics/ballActive1.PNG" border="0">
2. Yes you're right it's the animation. The ball collides with the water - it's collision box shrinks - it moves and collides again - shrinks - moves - collides ....
So the ball is colliding multiple times. Actually that boolean could come in handy here as well: (Another option is to disable collisions after colliding once)
<img src="https://dl.dropboxusercontent.com/u/8367729/construct/pics/ballActive2.PNG" border="0">
Oxyd_Enigma1_edit.capx