I've observed this consistently over the past few months. A script will run (fine), but the modal gray notification that "a script is running" continues to display in Sheets after the progress bar closes (because the script hit the end of its method, posted a complete status and returned), and when I look in the Apps Script dashboard I can see that the script is, in fact, still active. Periodically I will even get notices that such a script ended because it was timed out.
My assumption is that it has something to do with how the script is being invoked from the progress bar modal dialog generated by gas-lighter, but I have zero evidence to support this.