It's rather common that sometimes Spotify desktop client doesn't seem to scrobble to last.fm. Usually the missing scrobbles become visible a little later.
Disconnecting and reconnecting the last.fm application to your Spotify account should help clear things out as well. Make sure to remove the last.fm app from the list of your approved apps too before reconnecting last.fm to Spotify, you can do it here.
Are the scrobbles still missing for you? :)
Let me know how it goes!