Steps to reproduce:

1. Create a new Unity project
2. Import any texture and change it's type to Sprite
3. Open up Sprite Editor by clicking the button in the inspector
4. Dock the Sprite Editor window at the same place of another window, and open the other tab so the Sprite Editor would not be visible
5. Close and reopen the project
6. Select the sprite
7. Change any of it's settings
8. Click apply, notice it does not apply the changes and the NullReferenceException is thrown with each click

Workaround: If you focus the Sprite Editor window, and then click Apply, everything works normally after that.

See this screencast for repro steps: http://screencast.com/t/sLVfmO6bzlpe