Yes, it will give you the message if the upgrade is partial, since your
upgrade is incomplete. Certain packages can trigger the message since they
are considered part of the core distribution, but they are not essential to
running your operating system as you have found out.

Personally I remove all Mono from Ubuntu and this makes my computer not a
full Ubuntu distribution because Mono is part of the Ubuntu core. Tomboy and
F-spot require Mono. This is my do-it-yourself partial upgrade.