Looking at the RTL schematic view, the GUI incorrectly displays the following components:
The schematic in the RTL view has missing inputs that should be there.
The schematic in the RTL view also has missing inputs.
The design will still work correctly, but it will look unconnected in the RTL view.
Both of these issues have been fixed in the latest 10.1 Service Pack available at:
The first service pack containing the fix is 10.1 Service Pack 3.