Quick answer: You called Destroy on an asset from the Project window (a prefab, a shared material, a mesh) rather than on the instance in the scene. Keep the reference that Instantiate returns and destroy that. Never follow the message's advice to use DestroyImmediate(obj, true) in game code; it deletes the asset file.

This error is Unity protecting your project from a bug in your code. Somewhere, a reference you think points at a spawned object actually points at the prefab or asset it came from. The error message even suggests how to delete the asset, which is exactly what you do not want.

The exact error

Destroying assets is not permitted to avoid data loss.
If you really want to remove an asset use DestroyImmediate (theObject, true);

Cause 1: destroying the prefab instead of the instance

The classic version: you instantiate a prefab, but keep using the prefab reference afterwards.

public GameObject bulletPrefab;

void Fire()
{
    Instantiate(bulletPrefab, muzzle.position, muzzle.rotation);
    Destroy(bulletPrefab, 2f);   // error: this is the asset
}

// Fixed
void Fire()
{
    GameObject bullet = Instantiate(bulletPrefab, muzzle.position, muzzle.rotation);
    Destroy(bullet, 2f);
}

The same mistake hides in object pools that store prefabs in the “active” list, and in Inspector fields where a prefab from the Project window was dragged into a slot that should hold a scene object.

Cause 2: destroying a shared material, mesh or texture

renderer.sharedMaterial, meshFilter.sharedMesh and textures assigned in the Inspector are assets. Destroying them is refused. The copies Unity makes when you access renderer.material or meshFilter.mesh are instances, and those you should destroy when you are done, or they leak:

Material runtimeMat;

void Start()  { runtimeMat = GetComponent<Renderer>().material; }  // creates a copy
void OnDestroy() { if (runtimeMat != null) Destroy(runtimeMat); }

Cause 3: editor scripts modifying a prefab asset

Editor tools that remove children or components from a prefab asset directly hit the same guard. Load the prefab contents, edit them, then save:

string path = "Assets/Prefabs/Enemy.prefab";
GameObject root = PrefabUtility.LoadPrefabContents(path);
Transform old = root.transform.Find("OldVFX");
if (old != null) Object.DestroyImmediate(old.gameObject);
PrefabUtility.SaveAsPrefabAsset(root, path);
PrefabUtility.UnloadPrefabContents(root);

Finding the bad reference

Do not take the message’s advice

DestroyImmediate(theObject, true) permanently deletes the asset from your project. In an editor play session, that removes your prefab or material from disk. It exists for editor tools that intend to delete assets, never for gameplay code.

Related errors in builds

In a build there is no project to protect, but the same wrong reference shows up as MissingReferenceExceptions and objects that never get cleaned up. Bugnet's Unity SDK hooks Unity's log stream, so exceptions and errors in a player's build are filed automatically with the last log lines, a screenshot, the device, OS and build version, and identical ones stack into a single issue with a count.

Frequently asked questions

What does “Destroying assets is not permitted to avoid data loss” mean?

You called Destroy on an asset from the Project window, such as a prefab or shared material, instead of on a scene instance. Unity blocks it so the asset file is not deleted.

How do I destroy an instantiated prefab in Unity?

Store the return value of Instantiate and pass that to Destroy, not the prefab field you instantiated from.

Should I use DestroyImmediate(obj, true) to fix it?

No. That deletes the asset from your project. Fix the reference so you destroy the instance instead.

Instantiate returns the thing you own. Destroy that, never the field you instantiated from.