When running Toolkit actions in Shotgun you may see a Command Output frame pop up inside the webpage.
This pop up can be caused by two different scenarios.
The action that was run encountered an error, in which case this pop up will contain the details the error that occurred.
You have debug logging enabled. In this situation, the pop up will occur every time you run an action regardless of if there is an error. To fix it you need to disable debug logging.