System Information
Operating system:
Graphics card:

Blender Version
Broken: (example: 2.80, edbf15d3c044, master, 2018-11-28, as found on the splash screen)

When nodetrees get bigger, one might want to keep things tidy by calling multiple group input nodes in order to keep the noodles short, but the geometry nodes editor doesn't seem to like that.

Exact steps for others to reproduce the error
Inside the geometry nodes editor of a cube, add an instance node, instance something, add a transform node in front of it and duplicate the group input node. Now delete the transform node with reconnect. Notice how the cube turns back into a cube. Now delete the second group input node. The instanced objects are back again.