Is this behavior by design or a bug in Qt 4.6.2?
Before filing a bug report I wonder if this actually is wanted behavior. I found out that when you remove a QGraphicsItem from a QGraphicsItemGroup with removeFromGroup() method, the item removed gets selected status and QGraphicsScene's clearSelection() won't remove that selection. This happens at least if the group was selected before the remove action. You have to explicitly call setSelected(false) on the item after removing it to prevent e.g. specific painting. Just feels odd that clearSelection() does not work here. I'm using Qt 4.6.2 on maemo5.
That sounds (reads?) like a bug. You can file a report "here":http://bugreports.qt.nokia.com/.