The following limitations and workarounds relate to the Hypergraph.
A transform node displays the icon of its child shape when you hide or collapse the shape. Depending on the order the graph was built in, the icon may still occasionally show the transform icon, even if it has a shape child.
Workaround
Use Graph > Rebuild to update the icon.
Connections in the DG view can be deleted only when you single-select them. You cannot delete a multiple selection of connections with a single delete action.
Workaround
Delete each connection individually while you are in the DG view.
The IK Handle Tool behaves differently in the Hypergraph than it does in a model view. In a model view you can select the start joint and then select the end joint to add an IK handle. However, in the Hypergraph after you select the first joint you must hold down the Shift key to extend the selection for the end joint.