Pd-0.46-5-64bit.app comes out with permissions 555dr-xr-xr-x 3 phinze staff 102B Jan 19 17:43 Pd-0.46-5-64bit.app
So the cleanup operation after extraction is failing to remove the temporary dir.
Would it be possible to work with the maintainers of pd to get them to repackage their tarball with proper permissions? If not we can look into seeing if Cask can proactively chmod all extracted tarballs, but that seems like overkill if we can just get the maintainers to help us out."