Somebody is talking fast here.
It is claimed Kaspersky engineers took harmless Windows operating system files, manipulated them to appear as though they contained malware, and uploaded them to VirusTotal. The aim was to deceive non-Kaspersky antivirus engines into treating those system files as dangerous
I fail to see how this is possible. If you "manipulate Windows operating system files", they no longer ARE Windows operating files. And how does this deceive other antivirus engines? Does one mark certain strings in those files and tell the other engines "if you see those strings, quarantine the file"? And they do it? In the age of polymorphic virus, no less?
If you start getting false positives on OS files, then you have a big problem, and it has nothing to do with someone poisoning your well. It's more along the lines of being lazy or not having the right conduit to Microsoft.