You might be a bit out of your depth in understanding the issue.
The information is still a bit sketchy, but from what I gather, the chips in question are widely used to interface Arduino-type boards to your PC to program, debug, get data, etc...
The key thing here is that the counterfeit chips essentially have the same interface, so they can use the same drivers as devices built with the FTDI chips. Inside, however, they aren't using the same "firmware" as the FTDI chips, so the counterfeits have some extra functionality, like programmable PIDs; this is what FTDI exploited. It was NOT accidental, this simply isn't possible. They specifically coded their drivers to re-write the PIDs using functionality unique to the counterfeit chips.
The real problem is that they not only bricked the fake chips, but the entire device using it. This is a pretty bad thing, if your arduino was collecting data, for example, and you plugged it in to save it. The user has no idea his board is running FTDI-compatible chips (which is really what they are - they are no more "counterfeit" and an AMD CPU is somehow a counterfeit Intel CPU).
FTDI is upset because they paid legitimate fees to get the assigned PID for their device, but this is entirely the wrong way to do it. All you do is upset your customer base and break the law; destructive responses go back to the days when a CP/M spreadsheet program incorporated code to delete everything it could touch if it detected a pirated copy - and they paid dearly for that at the time. At least the victim back then WAS a pirate (mostly, unless the pirate was an unscrupulous vendor, which was often the case back in the 80s).