One of my kids had tried to download a few hefty games that saturated the available space to a point that I had no free space left at all. Download were waiting and the AppStore was requesting that I free up some space to complete the downloads.
I rebooted, deleted some apps and everything seemed back to normal. But after doing some math, it occurred to me that there was still a 2 gigs unaccounted for.
I eventually plugged my iPad 4 on my Ubuntu laptop, to see if the "Downloads" folder could be the stucked with old files in there. I was surprised to discover that a lot of data was stored in that folder but that the total size was 5.4 gigs!
From Nautilus, I manually deleted those files and got back more than I expected.
So If you suspect that your iOS device is missing some free space, have a look at the download folder...