### Godot version

v4.0.beta14.official [28a24639c]

### System information

Windows 10, OpenGL

### Issue description

Vulkan and Mobile:
![Godot_v4 0-beta14_win64_kEcRNiMfNJ](https://user-images.githubusercontent.com/7782218/213967627-8e8755d9-2fe2-43b3-b197-f9f2840b7580.gif)

OpenGL:
![Godot_v4 0-beta14_win64_MQ233TZuPq](https://user-images.githubusercontent.com/7782218/213967651-ae463a6f-c867-4312-bdf1-525e1d7def01.gif)

At first I thought it was related to `set_buffer()`, but it turned out that `set_instance_*` also work incorrectly.
Probably the custom information is also set incorrectly, but I haven't checked it yet.

### Steps to reproduce

* Open MRP
* In the editor, select `MeshInstance3D` node and change the `Count` property
* -- or --
* Start the project and move the slider

You can also switch the renderer to Vulkan and compare.

### Minimal reproduction project

[set_buffer().zip](https://github.com/godotengine/godot/files/10476834/set_buffer.zip)

Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND_V(!mesh, RID());
	ERR_FAIL_UNSIGNED_INDEX_V((uint32_t)p_surface, mesh->surface_count, RID());
	return mesh->surfaces[p_surface]->material;
}
RS::SurfaceData MeshStorage::mesh_get_surface(RID p_mesh, int p_surface) const {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND_V(!mesh, RS::SurfaceData());
	ERR_FAIL_UNSIGNED_INDEX_V((uint32_t)p_surface, mesh->surface_count, RS::SurfaceData());
	Mesh::Surface &s = *mesh->surfaces[p_surface];
	RS::SurfaceData sd;
	sd.format = s.format;
	if (s.vertex_buffer != 0) {
		sd.vertex_data = Utilities::buffer_get_data(GL_ARRAY_BUFFER, s.vertex_buffer, s.vertex_buffer_size);
	}
	if (s.attribute_buffer != 0) {
		sd.attribute_data = Utilities::buffer_get_data(GL_ARRAY_BUFFER, s.attribute_buffer, s.attribute_buffer_size);
	}
	if (s.skin_buffer != 0) {
		sd.skin_data = Utilities::buffer_get_data(GL_ARRAY_BUFFER, s.skin_buffer, s.skin_buffer_size);
	}
	sd.vertex_count = s.vertex_count;
	sd.index_count = s.index_count;
	sd.primitive = s.primitive;
	if (sd.index_count) {
		sd.index_data = Utilities::buffer_get_data(GL_ELEMENT_ARRAY_BUFFER, s.index_buffer, s.index_buffer_size);
	}
	sd.aabb = s.aabb;
	for (uint32_t i = 0; i < s.lod_count; i++) {
		RS::SurfaceData::LOD lod;