The issue #1, with a single item 'jumping out of it's grouping' seems to be related to picking an item back up and placing it down again. Ex, if you place an SRB in quarter symmetry, you'll see the icon with #4. If you then grab one of the items to move it around, then place it again, that one item's icon will now seem to be out of the group on it's own. Makes it a slight p.i.t.a for stage arrangements. But often if you leave the VAB or otherwise get the ship out of memory and reload it, all isolated items will be listed as grouped again.