I had the same thing happen on a 614ce Builders Edition about 18 months ago, right when that model was released. The 1st thing I noticed when I opened the case were 2 dimples about 1" apart. As the OP said, it was the "case's fault". I could feel 2 protrusions, presumably staples, under the felt lining in the exact spot where that part of the case would close on the top of the guitar.
I bought from Sweetwater, and they made the swap to a new guitar with no hassle at all. In fact, because the 614ce BE was so new, I had to wait ~3 weeks for the replacement, and they let me hold onto the blemished guitar in the meantime. Superb service.