End of the Line is multiball
But all the others are single ball. I wish I were more knowledgeable so I could help. I know some other Stern games use an infrared LED ball trough board to handle the kick outs. On Transformers, if this board malfunctions, or the LED or readers are dirty, or the leads need to be reseated, etc. it will kick out two balls into normal play. It seems strange if this is ONLY ever happening in Crank It Up though. In the times I've seen it (never on Metallica), it would be sporadic and not at all dependent on mode.
Edit: The part on TF is Dual Opto Transmitter #515-0173-00, and I see Metallica uses this same part. Page b3 of the manual: http://www.sternpinball.com/upload/games/metallica/pro/421/MTLAB1.PDF
That might be a lead into the issue. It was previously recommended to me to just replace the board if the foil traces are broken. If the connector is loose, just try reseating it. Some people have had to use cable ties to help hold the connector to the board on other games.