I've seen things like this before. Those directories - the ones
starting with "~" - seem to be used for backing up a package (it could a
dependency that is required by the package you are installing) before
installing a newer version. I think that somehow pip applies wrong file
permissions that prevent it from removing the backup directory at the
end. The issue does not affect the successful installation of the newer
version. I have been able to remove these directories myself afterwards
with no problems.