Согласно манам, dist-upgrade, помимо обновления самих пакетов, также обновляет связи между ними. upgrade оставляет неизменными пакеты, апгрейд которых затрагивает другие пакеты и связи. Достаточно dist-upgrade.
upgrade
upgrade is used to install the newest versions of all packages currently installed on the system from the sources enumerated in
/etc/apt/sources.list. Packages currently installed with new versions available are retrieved and upgraded; under no circumstances are
currently installed packages removed, or packages not already installed retrieved and installed. New versions of currently installed packages
that cannot be upgraded without changing the install status of another package will be left at their current version. An update must be
performed first so that apt-get knows that new versions of packages are available.
...
dist-upgrade
dist-upgrade in addition to performing the function of upgrade, also intelligently handles changing dependencies with new versions of
packages; apt-get has a "smart" conflict resolution system, and it will attempt to upgrade the most important packages at the expense of less
important ones if necessary. The /etc/apt/sources.list file contains a list of locations from which to retrieve desired package files. See
also apt_preferences(5) for a mechanism for overriding the general settings for individual packages."