If the game does not score a ball going into a cup the issue has to do with the ball score sensor. This is the 4 pin molex connector and the sensor is located on the underside of the cup assembly. 

1) Make sure that the balls are going thru the cup assembly and coming out to the ball shoot and the ben on the side of the game. 

2) If the balls are moving thru the game as it should remove the bottom ball plate from under the game. ( instructions are located in he manual with pictures).

3) Locate the ball score sensor (there are 6 on each side to make sure you know which on is effected) Have a teammate drop the ball thru the cup that is effected and make sure the ball passes by the sensor and that the sensor is not loose. 

4) If the sensor still does not score remove the sensor from the game and manually try and trigger the sensor. 

5) If the sensor still does not work test for voltage and if you are getting voltage test for signal from sensor. If no signal replace sensor. 

6) If sensor test good check continuity to the I/O board on signal wire and if continuity exits then replace input chip that corresponds to the cup location.