Prefabs are being overriden during runtime and destroying components is prevented?

I have about a dozen different Scenes in my project, with same scripts working correctly everywhere, except in this one particular Scene. There, adding components (box colliders in this case) to a prefab during runtime actually overrides the original prefab after Play-mode has ended, resulting in a prefab with half-a-dozen box colliders where there was none before. When these added components should be destroyed in a script, I get an error message ”Destroying assets is not permitted to avoid data loss.” This also applies to any instantiated clones that I make within the scene.

Also, in this Scene, it doesn’t allow to change the parenting of objects, giving me error ”Setting the parent of a transform which resides in a prefab is disabled to prevent data corruption.”

I want to emphasize that these same scripts and events work in every other scene, just not in this one. I’m wondering if this is a bug or have I accidently changed some Scene-specific setting from preferences or something. I’m hoping that is the case, but for the life of me I haven’t been able to find the answer from within Unity or from Google. Help is much appreciated!

Just in case anyone else runs into this problem, remember always to Apply new changes to your Prefabs if they work after editing, so you don’t end up using broken clones of them in new Scenes like I did… Case closed. :slight_smile: