iPhone 5S storage filled with "Documents and Data"
Short answer:
Restore to Factory Defaults
Long answer:
I had essentially this situation 3 weeks ago, although my capacity was &quot;consumed&quot; by Other.

iPhone 5S 32GB
iOS 9.3.2 (later updated to 9.3.3)
synced with iTunes 12.4.1.6
on Mac mini OS X 10.11.5

The iPhone Settings &gt; General &gt; About &gt; Available showed 0.25GB.
When syncing with iTunes, it showed unstable capacity numbers on each sync -- occasionally over-capacity with Other consuming 4.6GB, but settled down to 5.5GB available.  The 5GB discrepancy was concerning.
I tried:

rebooting =&gt; nothing
hard reset (Lock + Home, past Apple logo, to plug-in-to-iTunes image) &amp; update (re-install iOS) =&gt; freed 60MB
iOS update to 9.3.3 =&gt; nothing

The final option was what prior searching had said all along -- Restore to Factory Defaults.
I just followed Apple's procedure and it freed 9.5GB!
(Not sure where it came from, but I'm glad to have it back...  and disappointed that it was missing in the first place...)

Make sure your backup is current and you know the password, if encrypted.
Disable Find My iPhone.
Restore to factory (10-15min).
Went through the basic setup tweaks (it defaults to 6 digit passcode, now).
Restore backup (I enabled encrypted backups long ago and it took 4 tries to get the right password... oops!) (15min).
Authorize (iCloud?) from another device (my iPad).
Restore iCloud (It asked for iCloud security code or another authorized device.  I used the security code, which generated an iCloud Keychain verification code that was sent to the iPhone, which was in the middle of setting it up, so it showed momentarily and moved on.  Fortunately, it was mirrored to the Mac mini.  Then I never had to enter it...  perhaps a race condition with the previous step?)
Strangely, a few apps appeared to be installed, but a big sync with iTunes put everything where I expected it to be.
Finally, iTunes said 10.1GB free &amp; iPhone said 9.9GB free.  Not too bad.  So, yay?

Good luck.