How a bug in Skype prevented our users from using our app

Whoah, talk about burying the lede! TFA says that the root cause of the bug is Skype is adding tens of thousands of certs to the Trusted CA store on certain Windows boxen. Not sure what's worse, if it turns out that's a Skype bug or if it's by design...

On my machine I have, well had, one. What is going on here? Is adding a trusted CA cert (with the key) really a good idea?