1. In Universal Web adapter properties make sure "HookChildProcesses" ="true".
2. If you still face issue, let us know if the popup is chrome window popup or web based popup. A screenshot of issue causing popup would help me to answer. Depending on the type of popup based on screenshot, methods to interrogate varies.
As per the attached screenshot, ideally there is no need of any additional settings to interrogate the popup window, as it is html page. As per screenshot the popup have been hosted with windows.open(). Hence need more information.
1. Exact version of Robotics Studio and operating system you are using.
2. Enable verbose level logging and attach studio logs while interrogating.