How to reproduce:
1. Create a new project (e.g. Empty 3D project)
2. Open Build settings and switch to WebGL
3. Build and Run
Observe that build completes and opens in web browser
4. Click the close X icon to close the main Unity Editor window

What happens: Hold on (busy for xx:xx) dialog opens and remains open. The editor does not quit.
Application.Shutdown.CleanupMono
Waiting for Unity's code to finish executing

Workaround:
- Open Windows Task Manager.
- Find the Unity Editor process
- Expand it to show child processes
- Click the 'Node.js Server-side JavaScript' (choose the one that's for the build\WebGLSupport\BuildTools\Emscripten-win-x64\node\node.exe (you can right-click and select Open File Location to see which one this is).
- Right click and choose 'End task'
This then closes the Unity Editor.