I've had a few do this but don't view it as a problem...cases get thrown around on planes (or in UPS trucks). Affects some guitars more than others but it in the end the guitar still looks and sounds the same!
My Axis SS had these cracks within a month of when I bought it (about 10 months ago).
Since then I've flown it numerous times and they haven't grown or changed in any way. This kind thing just seems to happen a lot with bolt-on necks, but usually its not a problem. Make sure you have a good flight case if you're going to luggage check the guitar on a plane!
I have flown with my 20th Silo and no cracks at all. No cracks on my others either. The EBMM Polyester paint is thin and tough. Thin paint makes for good tone.