Why is Unity saving my modified transforms into my prefabs?

I started working on a project using Unity 2018.1.9f2 and for some reason when I apply settings to a prefab, it saves the position, rotation, and scale to the prefab. This sucks because when I instantiate that prefab, it has an offset from where I want it.

The Prefab documentation explicitly says this isn't how it should work:

However, you can also save overridden values from an instance back to the originating prefab using the Apply button (modified Transform position values are excluded for obvious reasons).

How do I get this project back to the normal behavior for prefabs?