Quoted from Rarehero:
If it's happening pretty much every time, there's most likely some kind of issue with your lower opto.
Not the lower optos. You need to hit the ball on the magnet hard, so it bounces up and triggers the upper optos. A weak shot (which triggers the lower opto) doesn't release the ball and will hold the second ball there until it times out.
When working properly, a hard hit will release both balls and add a third. If both balls get stuck on the magnet and it times out, you only get a two ball multiball. I had this wrong at first too. You can nail it hard enough to release from either flipper, but it's harder from the left flipper. Short answer: Aim better so you hit it harder.