This just isn't true. There's been plenty of lawsuits alleging that Amazon themselves sourced counterfeit product. Their supply chain for many products is not necessarily better than third party sellers.
It wasn't counterfeit (I don't think anyone is ripping off high-end TI calculators, and it also came with a license key for the computer software), but I believe it was intentionally incorrectly sold. It came in a blister pack and the paper insert inside plastic indicated it was the CAS model, but the calculator itself was the non-CAS model - in other words, aside from having the non-CAS calculator in the box, it was exactly identical to the CAS model as you would buy from a store.
Maybe TI mixed up their stuff but I doubt that; by that time I had already heard of Amazon selling counterfeit items and as you said there have apparently been lawsuits for this.
About a year later I had the exact same issue occur with another item - sold by Amazon, but fake, but got the right one after a return. Can't remember what it was though.
Everything is tracked by barcode. If it doesn't have a barcode matching what's expected, it doesn't exist anymore. Scratch a barcode the wrong way or mark it wrong, it loses it's ability to be scanned. It gets found, but what is it, inventory-wise?
The folks solving these problems, they're trained but some are better than others and it's not easy. There's 100s of millions of different ASINs. So they search by name and brand and say "looks like that's it" and voila, you have virtual inventory tracking this item as ASIN X, while it's actually ASIN Y.
No maliciousness needed. Just a complex system failing on the edge cases.
(Bias note: I work for another branch of Amazon. I do not speak for the company in any way. These are my own opinions.)