By default Ubuntu's docker setup uses AUFS for its storage layer. That leads to problems during startup because rename() may not work in AUFS.
To rename(2) directory may return EXDEV even if both of src and tgt are on the same aufs. When the rename-src dir exists on multiple branches and the lower dir has child(ren), aufs has to copyup all his children. It can be recursive copyup. Current aufs does not support such huge copyup operation at one time in kernel space, instead produces a warning and returns EXDEV. Generally, mv(1) detects this error and tries mkdir(2) and rename(2) or copy/unlink recursively. So the result is harmless. If your application which issues rename(2) for a directory does not support EXDEV, it will not work on aufs. Also this specification is applied to the case when the src directroy exists on the lower readonly branch and it has child(ren).
Starting the master may try to rename()
I think Kudu is supposed to fall back to copy/remove. As an example here is what python does