Is the save action occurring as a result of a script? Is this a save or a save as? Saves should take little to no time, unless over a slow network. It is not a good idea to work on InDesign files over a network, although everybody who knows this does it at least sometimes. Save As is usually a much longer process. When InDesign saves a file it appends the latest changes to the existing file, which requires little time. This has the effect of making a file take a bit longer to open, since there’s more data to read. Also the file is larger. A Save As forces InDesign to rebuild the saved file’s structure so there’s no changes added, so it’s a smaller file and it opens faster, although subsequent Saves should still be just as quick as will, of course, begin to increase file size.
Look as the script to see if it is using Save As instead of Save.