Object properties change on editor after running game

### Tested versions

Reproducible in versions 4.2.1 Mono and 4.3.dev5 Mono (these are the only versions that I tried)

### System information

MacOS 14.4.1 - Godot 4.2.1 - Mobile

### Issue description

## Object Property changes in editor after game is running

I do not why, but when I play the game seeing the scene where the bug occur nothing weird happen, but If I play the game seeing another scene but that scene actually contains the scene that presents the bug, well, after closing the game, the bug scene with the animator, change the object properties, in this case the position

https://github.com/godotengine/godot/assets/79183176/a6ece758-ba62-41ac-b4f3-877dfedbfa6d

### Steps to reproduce

The way its happened to me is having two scenes one with an animator that modify control's nodes position, add that scene into another scene and run the having the second scene open in the editor

### Minimal reproduction project (MRP)

[issue_project.zip](https://github.com/godotengine/godot/files/14799547/issue_project.zip)

Start with the issue_project.zip minimal reproduction and follow the listed two-scene steps on the affected Godot versions. Confirm whether running the containing scene changes the nested scene's Control node position in the editor, then verify that the editor properties remain unchanged after the game closes.

Written by the indexing model from the issue text.