The way the service works, is that you the vendor will ship your products into a amazon warehouse, other vendors will ship the "same items" a amazon warehouse, all of these "same items" are mixed together in the inventory system, your account is has a credit of "X items" but not the specific items you shipped in to the warehouse

Example

Acme Vendor shipped to amazon 15 Logitech MX Mouses

Evil Vendor shipped Amazon 15 Counterfeit Logitech MX Mouses

When amazon gets the mouses it take all 30 and puts them in a big box, as the orders are filled even if you ordered from Acme, you make get one of the one Evil shipped into Amazon

Amazon taking action against the vendor, and consumers blaming the wrong vendor.

When you order from Amazon Marketplace you can clearly see who you are ordering from, even if Amazon shipping the item. Consumers getting a bad product will then no only review the item but the seller with negative feedback even though the seller they bought it from may have done nothing wrong

Of course the real problem is the counterfeiters have no problem starting a new vendor every few weeks or even days, so the damage may already be done by the time the reports come back.