I mean, quite a bit of that stuff people pay premium for is already counterfeit even at stores like whole foods. I don't know how common it is, but it does exist.
My complaint is not just that counterfeit exists, but Amazon's lackluster response in dealing with it (here's your refund; now GTFO). Secondly, I'd guess that WF may have 1 ~ 2 suppliers for a given product, but Amazon may have hundreds, if they eventually allow 3rd party sellers. So they would have a harder time vetting their suppliers just by numbers alone. Finally, Amazon's warehousing policy of co-mingling stocks from different suppliers exacerbates the problem further.