If you are using CWM Recovery, boot into recovery mode and delete the CWM backup. You can also wipe cache partition and dalvik cache in the advanced option in recovery mode.:) It worked for me.
Just install this app and run it. Works like a charm. Then you can uninstall the app if you want.
There is an app called Delete Empty Contacts on the Play Store. I can't post the link here for some reason.
Facebook
Twitter
Instagram