The following script reproduces the issue: #!/bin/sh mkdir upper lower work merged upper/dir/ touch lower/test sudo mount -t overlay overlay -olowerdir=lower,upperdir=upper,workdir=work merged mv merged/test merged/dir/ rm merged/dir/test ls -l merged/dir/ The output from the last command is: /usr/bin/ls: cannot access merged/dir/test: No such file or directory total 0 c????????? ? ? ? ? ? test uname -a Linux linusputinmusk 4.2.5-1-ARCH #1 SMP PREEMPT Tue Oct 27 08:13:28 CET 2015 x86_64 GNU/Linux There is more information about this bug here: https://github.com/docker/docker/issues/9572
Proposed a fix upstream. http://marc.info/?l=linux-fsdevel&m=145252052703010&w=2
Fixed in 4.5 https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/commit/?id=45d11738969633ec07ca35d75d486bf2d8918df6
The Problem still exists in 4.7, see https://github.com/docker/docker/issues/25409#issuecomment-238524333
Can be seen in 4.3.5. Here, removing a directory always reproduces this issue. Subscribing for updates.