Baking UVs of a mesh with multiple textures produces one of the textures as the result

I’m not sure how to really phrase this question as I’m definitely attempting something above my ability.

I am trying to export a model, with multiple textures on it (if that matters), and was directed to baking the textures. I’m following most of the guides perfectly until I actually hit the "Bake" button.

The result intended was for a copy of the textures of the model but instead produced one of the textures that is being used in Blender, with a copy of the UV map over it.

Photo 1 is before being baked, and photo 2 is after being baked.

As you can see at the bottom of the second photo, Blender called back to texture already being used in the model, rather than the expected results.

Something might be glaringly wrong here but guides and wikis seem to be failing at mentioning it.

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Photo 1

Photo 2