on some filesystem(cramfs), empty file and empty directory have the same inode number. is_in_ino_dev_hashtable() only check inode number, so the second file/dir will be lost.
Fixed in git: commit 83bc4332e7d6d74293c1c41e047d2681a8350e1a Author: Denys Vlasenko <vda.linux@googlemail.com> Date: Tue Feb 25 15:27:58 2014 +0100 du, copy_file: fix file matching on cramfs