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.