Reproduction steps
1) Open "800186repro" project
2) Open "repro" scene
3) Notice that "Canvas" GameObject has 2 children: "Image" and "Image (1)", "Image (1)" has prefab
4) Enter playmode and notice that nothing changes
5) Exit playmode and delete "Image (1)" prefab in "Project" view
6) In Hierarchy view make "Image (1)" above "Image"
7) Enter playmode

Actual results:
"Image (1)" went back, below, "Image" GameObject.

Expected results"
"Image (1)" stays in the same place as before entering playmode.

Note:
This happens on all UI GameObjects and only when inside (as child) of a Canvas or any other UI element.

Workaround:
Brake prefab instance (GameObject > Break Prefab Instance)