I found the broken windmill in Skyloft and the guy told me that there used to be a smaller windmill but if fell off and into the clouds below. I know the piece and I remember seeing it back when I was obtaining the key parts for the Earth temple entrance.
I have travelled down and found the small windmill part but I can’t collect it. Is there something I am missing?
You won’t be able to collect the propeller until you have progressed further. You need to speak with Gondo first. He will go through the process on how to recover items that have fallen through the clouds.
Once you have done this you can go back to the windmill propeller and the robot will being it back to Skyloft for you.