It's a manufacturing defect from the supplier. Plus, I am guessing that the CGC has chosen to put the defect on the back of the inner well as opposed to the front. I don't believe unused inner wells have a specified front or back. That would be like specifying right and left socks.
It is my understanding from reading various posts on the boards that the CGC received a bad batch of inner wells from their supplier.
Instead of waiting for new inner wells from their suppliers, the CGC chose to continue under a "business as usual" mantra until the supplier of the inner wells rectified the problem. This left the CGC with an unspecified amount of defective (my word, not theirs) product to work their way through.
There actually IS a front and back tray member to the inner well. I don't think CGC is choosing to put the defect on the back. There are manufacturing reasons why this occurs. Please see my link.
LINK
It depends on which inner well is used. The modern inner well is pretty much a sleeve with both the front and the back being the same:
It doesn't not have the defect.
The inner well for this Bronze Age book is as you described; a tray with the book dropped into it and then the top sheet placed over it:
It does have the defect.
So, the next question would be is the defect only limited to the tray style inner wells or did I just get lucky on one and not the other.