[53ct10n8]

My LG Nexus 5 running veneno v9 and philz touch 6 says I've used nearly 12gb of 12.55gb. In settings under storage "other" says 10.xxgb, the files taking up that space are hidden and/or root. Disk usage app shows what appear to be multiple large partitions or directories that have files listed that were deleted either with usb connection to computer or factory data reset prior to downloading the disk usage app. It almost seems like there are multiple layers of old data that was deleted but never really totally vanished....
UPDATE: upon attempting deletion, i got the message "<file> does not exist" on everything that I attempted to delete, then it dissappeared. It was back again upon re-opening the disk usage app, however.

[RHTizzy]

Do all usage apps say the same? Just trying to think along... Sounds more like an issue with your OS though, not so much the Nexus

[53ct10n8]

I'm not sure to be honest, I've only used "Disk Usage" app, none of my file explorers show what I see in DU. Really wish I could post screenshots.