Comment 4 for bug 479638

The bug is triggered by un-grouping the group that contains the original circle (grouped with the character 'G').
a) individually un-grouping the groups containing a clone doesn't result in unexpected transformations.
b) manually removing the 'translate' attribute of the group containing the original circle and the character 'G' in the XML Editor before un-grouping all shows the revers happening: the circle and 'G' are translated by the same amount in the opposite direction as the clones are moved in you attached example 'binary_tree_mangled.svg' whereas the un-grouped clones stay in place.

possibly related or similar issues reported:
 bug #168651 "Tiled Clones" inside transformed groups broken
 bug #168286 ungrouping rotated group with text-on-path transforms text twice