The current problem had to do with the scaling of enemy characters being skewed because they were children of a scalable object. Essentially, the best prevention for this bug is to NEVER put enemy characters as children of anything with the exception of empty game objects that act as containers. I wanted to avoid using GameObject.Find() for triggering enemies with my trigger volumes so I had been relying on this.FindComponentsInChildren, but after a few scene saves the characters began to warp according to their rotation.
The previous bug led to the discovery that even empty objects with children can participate in collisions if their children have components capable of collision. So the best way to prevent my current problem is to make an empty game object the parent for both the enemies and the trigger volume. The collision for the trigger volume would be applied to the parenting empty game object, but the enemies would be at no risk of being magically rescaled while I am not looking at them.
In summary, I have made one step towards a best practice for anyone that uses a similar workflow to create trigger volumes in Unity3D. First create an empty game object for each trigger volume at the origin and name these containers for the specific encounters. Place any custom trigger scripts on these containers. Then create cubes or other shapes for your trigger volumes and make them children of the appropriately named container. Enemies can be placed in the scene in an idling state and be changed to their attacking state using the script on the container when the encounter is triggered. This is easy and cheaply accomplished by calling this.FindComponentsInChildren() and using a for loop to iterate through the array that is returned to activate each one in sequence.