In Debian and derivatives the auto-remove option only suggests packages that have been installed as a dependency of another package. If the depending package is removed, those packages are marked as auto-removable.
You don't have to run apt-get auto-remove
and the system will inform you happily about those packages for eternity. You can instead set them to be installed manually -- just run apt-get install <package> [<package>]
But your specific issue might stem from the fact that updating an unstable distribution might change dependencies and apt-get upgrade
does not account for that. Try running
apt-get dist-upgrade
which handles the upgrade process more intelligently (but also more intrusively.) Read the man page of apt-get
to get the full picture.