One reason for missing disk space (a scenario I just encountered myself because I obviously didn't do as I normally do when creating a new array), is this...
Usually I free all available disk space, also the 5% reserved for root (tune2fs -m0), since it's a single user file server system.
However, I was suddenly stuck with 0 bytes free according to df, but the difference between total and used space said something else.
Since I was certain I had freed those 5% reserved as a default in at least Fedora (and having some empty folders instead of having the files I had just copied... or thought I had), I started to sweat and search desperately for a way to fix this issue, rebooting, trying "lsof" and that kind of stuff.
Then finally I decided to run tune2fs -m0 on the file system even though I was certain that was not the cause - but it was! A little over 400G became available as it should be.
Yeah, I know... my mistake, but nonetheless my comment might be useful to others who forget about this reserved space or strongly believe they've freed it. c",)