iPhone Upgrade trade in “couldn’t be found”

I’ve been using the IPhone Upgrade program for a while now and decided to upgrade from a 12 to a 13. I was sent a kit to place my iPhone 12 in to send it back to Apple. I dropped it off at FedEx to send it back. I later got a call from Apple saying that the trade in box I sent in was empty. Now, I know for a fact I put it in there so I don’t know what happened to it. They said the box was “not tampered with” so no one could’ve taken it. I called back to open a case with Apple because I find it ridiculous that the phone is not in there. I even told them I have a receipt from fedex showing the box weighed .7 lbs so there’s proof it wasn’t empty. Well a month later after they closed the case, I’m getting charged monthly for the iPhone 12 I sent in. So I’m currently paying two monthly payments, one for a phone that I don’t have. Has anyone encountered an issue with trade ins/sending items back? Can apple track where it is based off the serial number? This has been so frustrating to deal with and it’s the last phone I buy using the IUP. I’m gonna try to see if I can dispute the charges with my credit card, although I paid for it with my Apple Card so I highly doubt that will go anywhere.