That doesn't surprise me. However, I'm 100% sure that this isn't a "Jeep-thing".
You can find that practice at virtually any manufacturer. That's how the system works.
A few weeks ago, I took my 2009 Lincoln MKZ in for scheduled maintenance. I bought it about a year ago as a certified pre-owned. The records showed that they repaired a rusted sub-frame during their CPO-inspection.
Well, guess what the service department found during the inspection: A rusted sub-frame and I was quoted $1,600 for a new one. Too bad the service-department was not aware of the fact that I had the records that showed that this issue was supposed to be "repaired" prior to me taken delivery.
In the end, I got a new sub-frame and the dealership and Lincoln agreed on paying for it 50/50. So basically, by quoting me in order to make money, they lost money. I wouldn't have noticed the rusted sub-frame on my own.
What I found most shocking was that the guy from the service-department actually told me that the sub-frame wasn't repaired during the prior CPO-verification - in his own words, he said it was simply "painted". WoW!