weird things can happen- not just at dealer level either. this sounds to me to be 100% a dealer coverup, but some can go farther.
my first ordered Mustang arrived after a 5 month wait, and a careless car hauler managed to let a ramp down on the rear wing, stuffing it a inch deep into the quarter...decklid/wing/quarter... car could not be 'received' by dealer couldnt even get a test drive- kinda sucked.
car was still technically consigned to shipper, and was taken by shipper to another ford dealer pretty far from mine for repairs, with damage noted in the file(had a guy at ford helping me track the car- last entry was documented damaged/for repair).
many months later, ran the vin thru another guy with carfax- car was sold in west virginia as a ford 'program' car (been a decade, cant recall the exact wording)with no damage documented at all!
to me, I think some form of interstate fraud might have been pulled off by either the shipper or higher up- someone bought a new mustang with a bondo'd/repainted quarter and either repaired or replaced(hopefully) decklid and wing. my dealer had said repairing was gonna require pulling rear/quarter glass, hammer/dolly/repaint blended to roof- possibly worse if any damage under the bumper/taillights to the structure.
lucky for me this happened- i figured out a while later had i bought that car it would have owned me- i was beyond obsessed about it...in the end it got reordered, and its identical twin has been a blast- hundreds of 1/4 mile flogs, etc, loved that car over a decade already, still as fun as that first (finally) test drive the day i picked it up...just a car, and it wont last forever, neither will i, have enjoyed the heck out of it....since, the wife got a matching 07, plus picked up another 'twin' to mine (except 2009) stashed away in storage for in case i might outlast the 06...if not, the kids shouldnt have much trouble getting rid of the virgin 5 mile car
hope this works out for you- if any help in your case, I could give you the details/vin/dates on that interstate 2006 repair/resold as 'new' one- whoever bought it got ripped off in my opinion, as the paperwork officially was all 'clean', but I have pics proving otherwise. whether it was ford or shipper, or the other dealer, i dunno- but for certain Ford regional KNEW that car was damaged, i sat in the office when my dealer was on the phone with regional about it...really pissed me off as they absolutely refused to talk directly to me about it, had to echo conversation thru dealer as i stood there...had my name on the DORA, had a deposit on it, was a weird day... but anyway think God just gave me a well deserved slap upside the head that day, as I had been completely obsessed about that stupid car for months before it even got built...