I don't know how it happens, but as I make changes, the order of GameObjects in the hierarchy become different to what they are in the Prefab. And then I cannot arrange them back because it pops up to say I need to "Open Prefab" to make changes to Prefab children. What I have is 2 levels deep prefab. Scene has Prefab A Prefab A is a variant of Prefab B When looking at Prefab A the order of GameObjects defined in Prefab B is not the same as in Prefab B. This has happened to me twice now. Last time I recreated Prefab A to fix it. I'm not sure if this first happened in 2018.3.0b6 or b7, but right now I am in b7. It is strange because I though you couldn't re-order children defined in a prefab, but here the prefab's children are re-ordered. It may be caused by me changing the order of children in Prefab B and then Prefab A got confused or something. Prefab A also adds new children and somehow they got in-between the ones defined in Prefab B.