I also ran into issues when trying to debug JavaScript in a PHP project. I was using Chrome as my browser and had confirmed that the Netbeans Connector extension was installed and working in Chrome.
I could debug PHP without any issues. I could create a separate HTML5/JavaScript project and debug JavaScript without any problem. However, when I tried to set breakpoints on JavaScript code that was embedded in tags within the PHP file, I would get the little 'broken' breakpoints that everyone else references. When I selected the option to debug project, I could debug the PHP code, but the JavaScript breakpoints were never hit.
The change that I made that finally (for me) caused the JavaScript breakpoints to be hit so I could step through code using the Netbeans debugger was to remove the Javascript from the file containing the PHP/HTML code and place the JavaScript in a separate file that only contained JavaScript via a within the PHP file. Magically, I could debug both JavaScript and PHP within the same debugging session without any extra setup.
Of course, one alternative is to use the debugger within the browser, such as Chrome developer tools, but I really wanted to be able to debug everything from within the same Netbeans environment. Works like a charm now.