Emulator

Update: Alternate method of triggering it

Load up a gamecube game with the Gamecube adapter for WiiU set
Create a savestate
Quit the game
Load up a gamecube game with the standard controller set
Load the savestate made with the GC controller, then within that small period, load the same savestate again
All input will now be broken

Update: Alternate method of triggering it

Load up a gamecube game with the Gamecube adapter for WiiU set
Create a savestate
Quit the game
Load up a gamecube game with the standard controller set
Load the savestate made with the GC controller, then within that small period, load the same savestate again
All input will now be broken

This method is both simpler to execute, and more likely to happen to the average user. It's easy to accidentally push the button twice, resulting in broken input.

I traced the code and found where the issue stems from. Not quite sure how you'd want this issue fixed so I'm not going to submit a pull request fixing it myself

Here's the important details

si.cpp
Within DoState()

    else
    {
      // If no movie is active, we'll assume the user wants to keep their current devices
      // instead of the ones they had when the savestate was created.
      // But we need to restore the current devices first just in case.
      SIDevices original_device = device->GetDeviceType();
      std::unique_ptr<ISIDevice> save_device = SIDevice_Create(type, i);
      save_device->DoState(p);
      AddDevice(std::move(save_device));
      ChangeDeviceDeterministic(original_device, i);
    }

And then in ChangeDeviceDeterministic

  if (GetDeviceType(channel) != device)
  {
    CoreTiming::ScheduleEvent(0, s_change_device_event, ((u64)channel << 32) | SIDEVICE_NONE);
    CoreTiming::ScheduleEvent(SystemTimers::GetTicksPerSecond(), s_change_device_event,
                              ((u64)channel << 32) | device);
  }

This is where the issue lies.

When you call ChangeDeviceDeterministic the first time, it disconnects the currently connected controller. If you then load the state again before it initializes the correct controller, the code in DoState to grab the currently connected controller grabs SIDEVICE_NONE as the controller had previously been disconnected. It then swaps the active controller to SIDEVICE_NONE instead of the correct device.