The ebuilds do wildcard expansion when installing: "${DISTDIR}"/${PN}*pdf or similar. Now the package manager may use the real DISTDIR, or it may use a "shadow" dir instead. The ebuild must not rely on either of these cases. If DISTDIR is the real dir, the ebuild will install any matching files, even if they are not in ${A}. For example, these could be files for a different version of the package. Please specify the filename explicitly. (AFAICS one single file is installed.)
*** Bug 613008 has been marked as a duplicate of this bug. ***
commit 1bfbb2fbe5f743bae7d83aa5e5849bf42efa25c7 Author: David Seifert <soap@gentoo.org> Date: Sun Mar 19 13:44:15 2017 +0100 sci-libs/scipy: Do not glob on DISTDIR Bug: https://bugs.gentoo.org/show_bug.cgi?id=612920