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.)