"Some nodes are referenced by animation tracks" when deleting instance

[KoBeWi]

Godot version

4.2 dev4

System information

Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1060 (NVIDIA; 30.0.15.1403) - Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz (8 Threads)

Issue description

#58598 introduced a warning when deleting nodes referenced animations. However, in very specific circumstances (which I couldn't determine) the warning will appear when deleting instanced scene, which is wrong:

I tried recreating the issue, but I wasn't able to. I have an affected scene that I could share.

Steps to reproduce

1. Open the MPR
2. Go to node_2d.tscn
3. Delete MudGolem

Minimal reproduction project

Wrongning.zip