System: Windows 19, Indesign 17.1
Steps to reproduce (though the trigger of this problem isn't known):
1. Open a file, change something. The asterisk next to the file name marks there are unsaved changes.
2. Hit Ctrl+s, then Ctrl+w to close. It will ask you to save again.
3. Cancel that requester and hit Ctrl+s again, plus Ctrl+w. The same.
4. Cancel again, then use the menu entry "Save", then hit Ctrl+w. Same story.

The asterisk remains and ID also doesn't lock as it usually does when saving (I'm not network, saving files take a few seconds). In this situation it would only save the file when you click Yes in the "Save the file?" requester after Ctrl+w.