This is a wag but I'd run switch test with one ball in the left lock, the t drop down and only 1 ball in the trough. I'd guess the second ball spot in the trough is reporting closed and the machine thinks it owes you a ball

Check the diode on switch 12 Lower Ball Ramp. I.e. the last trough switch before the shooter lane

That's sweet. I've been attempting to understand the switch matrix and that was the first time I was able to make the prediction about the problem.