New Upper A Arm Troubles

Pretty good, especially if they came off the same car. It could also be wasted bushings causing that issue, but the holes should be aligned. That doesn't mean that an acceptable alignment couldn't be done with those arms, either.
Just my two cents. Has the car been in an accident, if so the frame or ears may be bent. I'm referring to the used arm in the photo. I agree, the ends should line up, or the bushings will fail shorty. Like any business, you are only as good as your help. In this case, your supplier. Time to wake up or you will no longer have a business. Keep your customers happy. My take here for a positive solution is, the company that sold the defected part should contact the supplier and see if they can find another upper control arm from another company that they sold to and send the customer another one, DONE DEAL.