It may not be the guitar or the process. It may be from the fact that they are made in Indonesia, and they are shipped, in the winter, to Maryland.
So a story first. I found an amazing 95 CE22 and brought that baby home a dozen years ago now. I hadn't noticed it when I bought it but playing it at home I felt the fret sprout. I gave the whole neck a good rub down with lemon oil every day for about 3 days and the fret sprout went away and hasn't returned. The problem was that the wood had been exposed to very dry air and had shrunk. The lemon oil moisturized the neck.
Even though the necks are dried to about 8% humidity, in very dry air they can shrink even more. It's humid in Indonesia and dry in Maryland in the winter. Just rub in a few rounds of lemon oil or neck conditioner, and watch the neck swell back to original size.