So neither of these problems occur on your game (from clays site http://www.pinrepair.com/bally/9ball.htm ), and you never have the occasional problem where the bonus keeps adding up at the end of the 3rd ball forever? The pin knows the game is over, so it can't be some dirty switch..... :
The problem occurs after the numbered drop targets are hit (in order.) After the 5th ball drop target is hit (in order), and the ball is locked in the left side multi-ball lane, a new ball will be delivered to the shooter lane. If the shooter lane switch is not seen (because the switch is dirty or mis-adjusted or the player is holding the plunger, preventing the ball from closing the shooter lane switch), the game will continually kick balls to the shooter lane (causing an impromptu multi-ball.) This is weird because the player could have long sent the ball to the playfield, with the game scoring, yet a few seconds later, another ball is delivered to the shooter lane. Essentially the game gets "lost" and usually won't fix itself without draining all balls or doing a power cycle.
Another problem happens if say the #1 drop target is down, and as ball goes into the left multi-ball lane, it hits the #2 drop target (easy to do since the #2 target is at the lane entrance.) At this point the game should auto-drop the #2 target (a function of the left multiball trough lane), but the ball dropped the #2 target before going into the left side trough. Now the game will continually try and drop that #2 target over and over, looking for the target to drop (but it's already down!) There's no fixing this problem without a power cycle (or but sliding the glass back, lifting the #2 target, and letting the game drop it.)