They've probably noticed scuff marks on the inner arch. The front suspension is altered to suite the new front clip and wheels, the back inner arch has to carefully massaged with a hammer to allow enough room for the new larger wheels, you have to be careful not to split the welded join or metal. It's not hard if you're careful. There's also a seem along the top chassis by the top suspension mount, you may have marks up there aswell.
Sounds like this garage is being very picky if you've had the car on the road for so long without problems.
Are you near any of the DNA established mechanics? maybe they can advise