Stuxnet was a combined Israeli/US attack on Iran's nuclear capability. Kaspersky is a Russian security company which was started with government support, and is believed to still have connections there. Russia and Iran are allies.
Now look at how it played out. The US and Israel attacked Iran. Kaspersky tracked it down and publicized it to the world. And now some combination of the US, Israel, or close allies launched a spying attack on Kaspersky. Which, for all we know, may actually be an important part of the Russian cybersecurity infrastructure.
For all that organizations like the NSA do wrong (like spying on all of us), this is the kind of thing that we actually wanted them doing when they were created.