How to prevent resources being unloaded unintentionally

I have a folder with Prefabs in it and at the beginning of my game they are loaded using Resources.LoadAll and stored in an array. I use this array to instantiate gameobjects throughout the game and at some point, usually after a few hours (this is happening on my linux server) it seems as though they get unloaded and new gameobjects I instantiate from those prefabs throw a NullReferenceException when I try to access the transform.

Is this an improper usage of Resources.LoadAll? If not how can I prevent them from being unloaded?