Balls held in the upper lock after a drain is a game rule, not a fault
Multiball needs all three balls locked during the same ball in play. Lock progress does not carry over, so after a drain the game can leave balls sitting in the upper lock and play on with the ball from the trough. If two balls are locked and the game never feeds the third from the trough, clean and check the second lock switch.
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Source: Pinball Repair help group!! (Facebook group)