You will need to bend the piece of metal at the top edge of the trough to direct the ball downwards when it exits the trough. Otherwise the ball hits the other side of the shooter lane and bounces backwards. Here is a video of what is happening:
The ball feed from the shooter lane towards the ship targets can be adjusted by moving the lane guide. There should be a screw you can loosen which allows you to move the lane guide slightly; you may have to remove some plastics to get to it. Angle this so that the ball no longer travels towards the skull after hitting the targets.