My current vote for most annoying #WebStorm
Steps to reproduce:
1. Create a file in your project named index.js
2. Place a breakpoint on line 1 in it and start debugging
WebStorm will break on line 1 on every single index.js in the whole project.
Given that Node modules very commonly contain an index.js, you're now left unable to debug your problem.
And, yes, I know about the "Don't set into" options. But that isn't helpful when you explicitly need to debug third party modules as well.