[nitrogen]

Sometimes a newer version of package A will declare that it conflicts with package B. Maybe package C depended on both before the conflict was added. Then the package manager might find that the only way to resolve all conflicts is to remove C, which then auto-removes everything C depended on. Maybe C happens to be the "kububtu-desktop" package.

[piedar]

That seems like a poor design in apt. Does any other package manager allow such a thing? I know Arch's pacman has no autoremove - you have to gather a list of unneeded packages then remove them as a separate step. And Gentoo's emerge builds a dependency tree rooted in the @world package set, so if kde-plasma/plasma-meta is there it will never be removed by an automatic depclean.