He also said he tried to re-order them, and they were already sold-out. Had to buy it online and pay shipping.
Is this a comic shop or just a shop that buys comics ... like a gaming store or book store? I ask because you have said he also keeps no inventory and never orders more comics than his customers do.
It's a "collectibles" shop. Comics, sports memorabilia, gaming cards, autographed framed photos, etc.
He does order a handful of extra comics, on the top highest selling titles only. But for the most part, he orders enough for his pre-order customers, and if you aren't there on Wednesday, when comics go out, and you didn't pre-order it; then chances are you aren't gonna get it.
However in this case, I don't think he's ever made a mistake that big. This was a one-time screw-up.