When using groupings, new functionality lets a teacher assign resources and activities to groupings, thus making them only available to certain groups of users.

This is not reflected in the gradebook -

Create a few groups and at least one grouping, then assign one of the groups to the grouping. Create a graded activity and assign it to the grouping.
When you look at the gradebook, the activity is listed under all the group views, and if you edit the category and uncheck 'Aggregate only non-empty grades', then this item will be counted as a zero for students that are not in the grouping.

I think the best answer is that items assigned to grouping need to have some sort of visual indicator that they are assigned to a grouping, editing on that item should be disabled for students not in the grouping, and there needs to be a check of some sort so that activities assigned to groupings are only included in any grade calculations if the student is part of that grouping.

Not sure if the gradebook should change according to the group display - or if this may need to be an option. It makes sense to NOT display the grouping activity if you are looking at a group that isn't part of the grouping, but that may lead to confusion if you're trying to line up gradebooks for different groups and forget that it's a grouping-specific activity.