The math desktop file should not be installed as it is just trivial extension that users usually don't want to run themselves. 3.3 did not install this, since 3.4 it does so. this needs to be adjusted in distro-pack-install to not be installed. I suspect bin/distro-install-desktop-integration for this one.
I have added NoDisplay=true in math.desktop. The desktop file still makes sense to define the MIME type association. The fix is in master, see http://cgit.freedesktop.org/libreoffice/core/commit/?id=369f22ceb8b3440d8caf1d60d7f45abc1d5ac258