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When I look at the storage section of my phone, the various categories add up to about 2.5 GB of storage, but it says that 11.4 GB is being used. Is there any way to figure out what else is taking up space on my phone?

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Since the upgrade to iOS 9.2, I have noticed that my backup size has been growing by 100MBs with every sync. No amount of health data, mail or messaging can account for this. I believe it has something to do with the feature in iOS 9 which allows documents and data from applications to be backed up to iCloud Drive outside of the iPhone backup menu.

This "helpful" feature to iOS appears to store the documents and data accumulated by an app not only in the iPhone's local storage but also in your iCloud quota even though it is not transparent that it is doing so. Since for many apps, this local cache is many times larger than the application files themselves, it is possible that this is responsible for the rapid, undocumented, and unconfigured consumption of iCloud quotas.

Settings > General > Storage & iCloud Usage > Storage > Manage Storage > [any app]
App Size: 59.3 MB
Documents & Data: 47.5 MB

Settings > General > Storage & iCloud Usage > iCloud > Manage Storage > This iPhone > Backup Options > [any app]
3.8 MB

Settings > iCloud > iCloud Drive > On
Allow apps to store documents and data in iCloud

Unfortunately, I have tried to delete and reinstall the most nefarious offenders and even though it has opened up over 2GB on my local storage and turned iCloud Drive off, the iPhone backup process has yet to recognize this adjustment. I do not know if this is a problem with the iCloud/iPhone negotiation process, or corrupted settings on my phone. But, this feature is the only feature that I have found that even comes close to adding up the 'missing' amount of data which is hogging up my quota.

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Please check out What is other on iPhone Storage to get a nice way in finding your hidden storage waste.

Also to give you a nice way to fix this. Restore your iPhone to the most recent version and then place the backup file back. Don't just update as it won't remove anything.

Also check out this Apple KB about the space issue.

To summarize Apple's solution:

  1. Turn off the music or photo sync option in iTunes for the device.
  2. Click Apply to sync the changes to the device.
  3. Turn the music and photo sync options for the device on again.
  4. Click Apply again to try to sync the device to iTunes.
  5. If the 'Not enough free space' alert appears, continue to step 5.
  6. Turn off the automatic syncing functions for the iOS device. To do this:
    1. Select the iOS device from the iTunes window and click the Summary tab.
    2. Deselect "Automatically sync when this device is connected" and select the "Sync only checked songs and videos" checkbox.
    3. Click Apply to sync the changes to the device.
    4. Reduce the amount of data that is being synced to the device and resync the device. For example, if syncing your Music library exceeds the memory capacity of the device, choose "Selected playlists" to transfer rather than "All songs and playlists" under the Music tab in iTunes. If the 'Not enough free space' alert appears, continue to step 6.
  7. Restore using iTunes.
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Links can break rendering answers which link to external sites quite useless. Can you please include the essential part of the referenced page directly into your answer to prevent this? – patrix Apr 14 '14 at 6:44
@patrix I've added a second (official) source plus steps. – Rob Apr 14 '14 at 6:54

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