Trust me, I'm just as OCD as you are about this stuff, so I can relate.
However, Vibram has had a lot of QC issues (at least they have in the past...I haven't bought a new pair recently), so if that's the only flaw and the seams or other things don't fall apart after two weeks of wear then count yourself lucky. How big is this spot, anyway? It's hard to tell, but from the photo I'm guessing it's a few millimeters. If it really is that tiny I'd say don't worry about it, and once you've worn the shoes a few weeks you'll probably forget it's there.