It's getting hard to know what's happening since iTunes often shows more then 2 to 10 GB of difference on the "free space" number that iOS self reports.
The iOS system has four categories of data:
- third party application data that is marked as "purgeable"
- third party application data that is marked as "non-purgeable"
- application cached data which is there for speed and will be cleared when you run low on space / regenerated when you launch that app again
- Apple's own iCloud data
When I'm in a low space situation, here's what I do:
- look for easy things I can delete - entire applications (podcasts or apps, video & movie downloads or turning off big users like iCloud photo stream. Things I don't need when I'm facing a recurring prompt and that will re-download overnight when I'm in WiFi range.
- turn off iCloud backup (I think, but can't prove there's a bug there on iOS 9 leaking storage space)
- put the device in AirPlane mode
- power of the iOS device
- restart the device
Then I re-examing the free space on iOS and compare with iTunes if I can. If you can get 2 GB of free space, things usually level off. Less than that, and every app you start can and will re-populate the caches and temporary space and you'll likely be back to "no space".
I would set a calendar reminder to turn on iCloud backups in 24 hours - but make sure it's not depending on iCloud sync so that you can check storage space before you toggle that back on. I typically make an iTunes backup before turning it on.
The next step for me when the device isn't managing things properly is to erase the device and not restore the backup - so archiving that backup is a nice safety net if I find in a week I didn't have everything transferred off the phone.
Archiving means first making a backup in iTunes and then control-clicking on the backup itself in preferences and choosing to Archive it. Things to consider are:
- health data only is saved to an encrypted backup
- transferring purchases helps you not lose apps or data in apps if they are removed from the store after you installed them or after you complete the backup
- some account and WiFi passwords and certificates are not saved to unencrypted backups
The archive feature prevents newer backups from overwriting the archived backup. The downside is the backup takes up more space than one that gets cleaned up/changed the next time you back up to iTunes.