iCloud storage

Hello Mr3giphone,

It sounds like you are getting a message that you are out of storage space in iCloud so you cannot back up your phone, but you have deleted all your backups stored in iCloud. I recommend this section in particular of the article named:

iCloud: Troubleshooting storage issues

http://support.apple.com/kb/TS4009

Inconsistent values

Documents in the Cloud

If you add files to Documents in the Cloud using any method other than the recommended iCloud iWork Pages, Numbers, or Keynote web apps, App Store approved applications, or through the iCloud Documents Library on your Mac, the amount of storage available for your iCloud account may be inconsistent on your iOS device or in System Preferences.

To resolve this issue, do one of the following:

• Go to iCloud.com, select the Pages, Numbers or Keynote app, then locate and delete the files.
• From your iOS device (iPad, iPhone, or iPod touch), go to Settings > iCloud > Storage and Backup > Manage Storage, then locate and delete the files.
• On your Mac, choose System Preferences > iCloud > Manage, then locate and delete the files.
• On your PC:
  • In Windows 8, go to the Start screen, click the iCloud tile, click Manage, then locate and delete the files.
  • In Windows 7 and Vista, choose Start > All Programs > iCloud > iCloud, click Manage, then locate and delete the files.

After you've deleted the files, the change to the amount of storage you have available updates automatically.If you're unable to locate or delete the files, or the amount of storage you have available in your iCloud account continues to be inconsistent, contact iCloud Support for assistance.iCloud BackupIf you turned off iCloud Backup and do not see your available storage increase as expected, try the following:

1. From an iOS device that does not have iCloud Backup enabled, choose Settings > iCloud.
2. Tap Storage & Backup.
3. Turn on iCloud Backup.
4. Tap Manage Storage.
5. Select the name of your device under Backups.
6. Tap Delete Backup, then tap Turn Off & Delete.

If your available storage displayed in iCloud Settings on your iOS device, in iCloud System Preferences on your Mac, or in the iCloud Control Panel for Windows on your PC continues to be different than expected, contact iCloud Support for assistance.

Thank you for using Apple Support Communities.

Regards,

Sterling

Thank you for the update!

So you have done all the troubleshooting in the article? Alright, next I would reach out to our iCloud Support for additional assistance with this discrepancy.

iCloud Support

Click the link, choose your country and it will walk you through getting in touch with the department.