Pop up requests not turning off.

When a new or upgraded application is started we often get a pop up request to change some permissions or the like. at this point occasionally the whole application will hang. If we go to the Activity Monitor and force quit the application, the pop up notice will remain on the screen. If you run through the process again and the app hangs both notices will remain on the screen.

Is there a way to clear them? Example of pop ups shown as I was writing this.