You need conditions to pick the turrets that blow up. In your conditions, you probably already reference the ship, so the game knows which ship to destroy. If you add an action to destroy turret without picking any, it is assumed that that action will be applied to all turrets.
Try adding the condition turret is overlapping ship.
Utilizing containers is a good way to work around this as well.
There are many many ways to implement reloading, so without any further detail on the specific behavior you want I'm going to just suggest you run a quick search. Generally it involves a counter variable to keep track of ammo remaining and some events to handle what happens in different "states" (ammo full, partially empty, empty).