Godot version:
v3.0.2.stable.official
OS/device including version:
Ubuntu 16.04.3 LTS
Issue description:
When I change margin for any child node which is in some Container so after run
scene the changes doesn't show..:
margin-test-video.zip
And after restart Godot are margins reseted in inspector although in main.tscn are different values for margin..:

Steps to reproduce:
Open Minimal reproduction project -> change some margin of any label -> run scene
Minimal reproduction project:
TestMargin.zip
As far as I understood this is intended, you should set the margins in the container and not in the children inside it.
@legione Where in the container?? When I have more containers in one container as children it is same problem..
I want have to the result in game same as in the editor..:

This this expected behavior, the containers override their children margin and anchors values.
And yeah, the editor should prevent you from modifying the position or size of children nodes. That will be implemented someday.
If you resize the container in the editor you will see that the content will adapt.
@groud OK and When it will be implemented that editor prevent modifying the position or size??
This is very confusing for beginner users...
I hope that exists somewhere ticket for this.. or not??
Reduz is reworking the inspector, this is the first step before such improvements.
Most helpful comment
Reduz is reworking the inspector, this is the first step before such improvements.