How do you put a kill switch in? The entire point was for it to be on an offline system, and the traffic for it checking for Internet to in turn check for an order like that might have given the game away.
It sounds like they had something to check it wasn't outside and someone just screwed up.
I think the obvious thing would be to look for Internet activity on the machine. E.g., recent files for popular sites in a browser cache directory. Or live network traffic for public netblocks.
But it has to start out on machines connected to the public internet before spreading to the secret facility via USB drive. If it didn't spread when connected to the Internet, it wouldn't work. And it already doesn't blow up centrifuges when it's not on the target network.
You engineer a solution. Quite frankly if you can't think of how to put a kill switch into something like this then it shouldn't be getting written or allowed into the wild. You can't add that to Bugzilla and hope to fix it later.
It sounds like they had something to check it wasn't outside and someone just screwed up.