How to trigger it:
You open the “Add-ons” window and check for new add-on updates, and new ones are actually available. You choose to update the add-on.
As a result, a new window with a progression indicator is displayed. While this window is open, you close the “Add-ons” window in the background. However the window with the progression indicator will stay open, until the add-on updated. After it finished updating, the window with the progression indicator will close, leaving you with only the main window open. However the main window will refuse any input, making it seem like you didn’t close “Add-ons” window, which you did however. The only option to escape now is to force-close Anki.
In fact this bug also happens, when you simply try to install an add-on, and you close the “Add-ons” window in the background, I also uploaded a video showing the bug here.