Godot opens popup like AcceptDialog even if project is not running

[qarmin]

Godot version:
4.0.dev.custom_build.5f1107aa3

OS/device including version:
Ubuntu 19.10
Issue description:
When I open project, then 2/3 popups shows, which should be visible only when project is running.

Minimal reproduction project:
Just open project - https://github.com/qarmin/The-worst-Godot-test-project

[Anutrix]

I tried to open the test project in v4.0.alpha.custom_build [3fe3c43] but it asked me to convert it(which I accepted). Even though I got a lot of errors, the bug could not be reproduced.

@qarmin If this bug is reproducible, please upload 4.0 version MRP.

[qarmin]

Also cannot reproduce with latest version