When that happens, there are two other options:
- File > Add to Sidebar
- Keyboard shortcuts
Sometimes the File menu option is not available, but the keyboard shortcut CTRL + CMD + T is usually right to go.
You could try dragging a subfolder into place and then ESCAPEing out of it. This will usually open up the past the re-add the folder you couldn’t add a moment ago.
reference: http://apple.stackexchange.com/questions/139305/how-can-i-add-new-folders-to-the-favorites-in-the-finder-sidebar/226776#226776