When using Tiny Core Linux I found that du was counting hard linked files as different.  Getting coreutils.tcz fixed the problem but the base is still incorrect.

Test:

printf "% $((12*1024))s" '' > file1
cp -l file1 file2
cp file2 file3
ls -li file*
du -sc file*


Expected that du either doesn't show file2 or reports that it is smaller in size.  ls shows that the inodes of file1 and file2 are the same.

Expected result:
 818936 -rw-r--r--    2 backup   backup       12288 Jun  6 08:52 file1
 818936 -rw-r--r--    2 backup   backup       12288 Jun  6 08:52 file2
 818945 -rw-r--r--    1 backup   backup       12288 Jun  6 08:52 file3
12      file1
12      file3
24      total

Received result:
 818936 -rw-r--r--    2 backup   backup       12288 Jun  6 08:55 file1
 818936 -rw-r--r--    2 backup   backup       12288 Jun  6 08:55 file2
 857130 -rw-r--r--    1 backup   backup       12288 Jun  6 08:55 file3
12      file1
12      file2
12      file3
36      total