I've seen this happen with a machine on location believe I now know the cause, some of this information is what I've personally experienced while some is from deductive reasoning.

What I have seen happen is that a rapidly moving ball entering the ball lock off the left flipper can become airborne after hitting the back edge of the play field lock channel (bare wood cutout on topside of playfield), this ball then rides up the one-way gate for the skill shot and wedges itself between the upper playfied and the playfield plastic. Having a ball stuck in this location now prevents the one way gate from opening and any ball entering from the skill shot or dropped into the lock from the upper playfield will backup behind the gate.

With these balls sitting behind the one-way gate, the balls dropped from the top will now sit atop the blocked balls. I have also seen a solo ball wedged between the mini-playfieds wiring and a main playfield plastic blocking just the elevator drop down hole; I speculate that this ball was jammed into this position similar means that caused the one-way gate to become blocked in the first place...A rapidly moving ball striking the gate would transfer its energy through the balls behind the gate (think Newton's Cradle) this energy would thrust the ball sitting on top of the others upwards and away jamming it in a position that no ball should be able to get to on its own.

The fix for this would be to install a post or bracket to either the underside of the mini-playfield, or on top of the main playfield to prevent a ball from blocking the gate. The trick here is going to be finding the right spot to install it without interfering with the other moving parts of the game.