When you complete any stage, all loaded resources are gone. And inserters will always load excess material.
Possible solutions:
1) Switch to different recipe at the end
2) Make stages in between (like "stage 2.5") for unloading resources (copy inventory before upgrading, switch to intermediate stage, place copied things to inventory)

+1 for this issue
this is especially annoying with Space Exploration as you need to move all needed ressources to another planet.
I have calculated what ressources are needed and take them with me exactly. When some ressources are just lost in the stage change, you need to go back to your home base and again to the new plant with another rocket to get the lost ressources.
I think the second solution proposed by ItramariN sounds pretty good!
Just setting the output slots to the previous input slots and then waiting for them to get emptied in an intermediate step should resolve this issue entirely!