I have a Sony Xperia SL with 32 GB internal storage from which 25 GB is available for user. When I bought the phone, everything was OK. but last month I found out that there is only 1GB left free, when sum of the files in the memory was only 21GB. I deleted some files and reduced the filled capacity to 10GB. However, I still have only 12GB free on my device. It sounds like 3GB of my storage is lost. (I have checked LOST.DIR and, for those who want to know, I have considered the thumbnail files when I summed up the files)
When things with storage go awry I use DiskUsage. It uses a graphical interface (hardware or software rendering), very intuitive. You can scan (look at) multiple areas. With this app you will be able to isolate (locate) the problem. After finding the space hog, you can delete within the app or use a file manager to perform more complicated tasks. Root will allow viewing system locations.
I don't work/publish/design/develop/etc. on this app, nor do I receive any compensation for anything related to this app. It's just very useful
As always perform a backup before deleting anything
It might be some directories itself where the space ist lost. If you deleted a lot of files in a directory, the space is freed, but the space for directory entries is not reduced. You can help yourself with this (in a terminal):
mv dirname dirname.old
mv dirname.old/* dirname
This should give you back the lost space.