I have notice that
ls -l reports the physical size for a directory while it reports the logical size for a file. For example this is a sample output from
drwxr-xr-x 2 chris chris 36864 2017-04-23 18:14 dir1 -rw-r--r-- 1 chris chris 6 2017-04-23 18:10 file1.txt
dir1 size is 36864 bytes, which is a multiple of 4096 bytes (so it is probably the physical size).
file1.txt size is 6 bytes (which is the logical size).