Set missing all the Minifigures and a few other parts
It is unlikely that Lego mispacked all of the minifigures. In the Quinjet set, the figures are spread among several bags, meaning Lego would have had a packing error in multiple bags, and then coincidentally placed all of the mispacked bags into the same box.

More likely is that someone removed them from the box and returned the package to the store. If I were you, I would take the box back to the point of purchase and ask for a replacement. The set is still in production, so they should be able to get you another or refund your money.