Check the trough switches so it knows how many balls are in the tough.

Check the shooter lane switch to make sure it knows if gave you a ball.

Check that neither of the two saucer switches are stuck closed. If it thinks you locked a ball it will give you a new one.

Quick way to check the saucer switch theory. Start a game and after the second ball pops out run your finger over the top skill shot switch. If the pops do not start flashing it thinks another switch (saucer) has been hit and the skill shot becomes unavailable.