However, a lot of manufacture is contracted out. If you're buying 10 or 20 chips for internal R&D you'll likely get genuine ones.
However, when you find a contract manufacturer and ask them to make 100,000. You require an XYZ, Inc. ABC123 chip and ask the manufacturing contractor to source it. Unbeknown to you, they obtain a counterfeit source. The chip is virtually identical externally, and functionally very similar, so that your product passes validation testing.
You as the device designer and seller may have no idea that you have fake chips on your device. Perhaps, your RMA rate is higher than you expected due to chip failures, or perhaps you are getting a lot of bug reports from the field which are not reproducible on your prototypes, but are on production devices.
This isn't the first time a USB->UART vendor has taken vigilante action against fakes. The vendor Prolific had major problems with low-quality, buggy and slow fake chips, causing major support headaches for customers and themselves. I believe they ended up discontinuing their main product and replacing it with an incompatible version, while poisoning the drivers so that they would BSOD/Kernel panic if they detected a fake chip.