I don't know why anyone is surprised by this. Historically it seems Apple has never had inventory to meet demand the first few weeks or even months. When the 6+ came out I couldn't find one in my desired configuration anywhere in the Southern California area for two months. I happened to be traveling and finally found one in San Luis Obispo in late November, and based on the online inventory sites I'm pretty sure they were the only store in California that had any of the Space Grey 128 GB Plus models.
You would think with a giant company like Apple they would be able to correctly estimate demand and produce enough units that anyone could walk into an Apple or carrier store on launch day, or launch week, and be able to get whatever color/config they want. They should also know by now that the new colors are always the most in demand. So why the shortage of Jet Black? I got my pre-order in during the first 10 minutes and my delivery date is still September 23 or after. I know the assembly lines can only crank out so many units a day but it's still ridiculous having to go through this every year. Really at this point no one should have to get up at 3 in the morning or camp out overnight to get an iPhone.