You could pull the apron and watch how the balls move around as they are kicked out. It could be that the process of kicking out balls pushes the remaining ones in the trough backwards, which could confuse the machine.

Other wise, I think that there is a fix using a trough liner or the file, as you suggested.

In thinking about it a bit more, you may have a problem with the trough opto boards. Put the machine into switch test and bang on the playfield. Continue by removing one ball at a time while thumping the playfield and see if any trough switches change from open to closed, or closed to open.

Since multiball is supposed to be 3 balls, perhaps the machine is not seeing that it should be kicking another one out.

not too hard. it would be like the combined vibration of a slingshot going off at the same time both flippers are activated. basically, just enough to jar the trough optos.

Correct about the general multiball.

I believe that Crime Wave and Midnight Madness are 4-ball multiballs. The Warehouse offers one or, perhaps, two different 2-ball multiball modes.