WHy do I lose some scripts when quitting the player?

I have a project which loads assets bundles during the editor and it also reloads them during the player. A couple of those assets have scripts attached which all work perfectly well in the editor and during playmode (in the player).

However, as soon as I quit play mode, I notice that some of the gameobjects (which were instances of downloaded assets bundles) have lost their monoscripts which where previously attached. (The inspector just reads MonoBehaviour script Missing)

Oddly, the public variables of the now missing script are still displayed in the editor.

Any ideas?

Edit: In addition, I've noticed that my prefab's meshes also vanish when I press stop on the player. How can I prevent this and why does it happen?

Thanks