This is a regression caused by Bug 74064.
While in Gnome 3,
1. Open an existing ods document,
2. Go to File -> Save As, and make sure you have the GTK's native file dialog open.
3. Change the format type to anything other than ODS, say, Microsoft Excel (.xls).
4. Hit Save.
It still tries to save the document as the original ods document.
I chose to revert the "fix" for fdo#74064 for now.