Comment 2 for bug 1583591

This is an explicit feature – apt will mark the packages as manual if the metapackage is removed as a consequence of another package (e.g. you remove the browser the metapackage depends on, the office-suite will be marked as manual to prevent it to be removed automatically just because you don't like the browser).

If you request the removal of the metapackage explicitly through, the dependencies will not be marked. You can do that manually as you see fit. This is done so that people who install a suite of packages via a metapackage can get right of this suite in (roughly) the same way they installed it.